| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 194/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.5.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: biodbChebi |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbChebi_1.5.0.tar.gz |
| StartedAt: 2023-04-11 18:52:27 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 18:54:57 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 149.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbChebi_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbChebi.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.5.0’
* 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 R 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbChebi.Rmd’ using ‘UTF-8’... OK
NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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 [2023-04-11 18:53:11.489][biodb::testContext]
biodb.INFO [2023-04-11 18:53:11.492][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:11.493][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-11 18:53:11.494][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:11.495][biodb::testContext]
biodb.INFO [2023-04-11 18:53:11.513][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:11.515][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:11.524][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:11.525][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:53:11.526][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:53:11.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.530][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:53:11.551][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:53:11.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.555][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:53:11.556][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:53:11.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.560][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:53:11.561][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:53:11.562][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:53:11.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.566][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:53:11.567][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:53:11.568][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:53:11.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.572][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:53:11.573][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:53:11.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.576][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.DEBUG[2023-04-11 18:53:11.577][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:53:11.578][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:53:11.579][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:53:11.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.583][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:53:11.584][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:53:11.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.588][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:53:11.589][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:53:11.590][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:53:11.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.594][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:11.595][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:53:11.596][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:53:11.597][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:53:11.598][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:53:11.599][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:53:11.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.603][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:53:11.604][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:53:11.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.608][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:53:11.609][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:53:11.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.613][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:53:11.614][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:53:11.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.618][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:53:11.619][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:53:11.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.622][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[2023-04-11 18:53:11.623][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:53:11.624][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:53:11.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.628][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:11.629][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:53:11.632][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:53:11.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.635][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[2023-04-11 18:53:11.636][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:53:11.638][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:53:11.639][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:53:11.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.646][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:53:11.688][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.726][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:53:11.727][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.728][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:11.729][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.733][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.734][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:11.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:11.736][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.737][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:53:11.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:11.739][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.741][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:11.741][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:11.741][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:11.741][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:11.741][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:11.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:11.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.745][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:11.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.749][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.750][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:11.751][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:11.752][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.753][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.754][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:53:11.756][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.757][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:11.758][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.759][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:11.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.763][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.764][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:11.765][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:11.766][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.767][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:53:11.768][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:11.769][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.771][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.772][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:11.772][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:11.772][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:11.772][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:11.772][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:11.773][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:11.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:11.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.779][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:11.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:11.782][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.783][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.785][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:53:11.786][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.787][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:53:11.788][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.789][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:11.790][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.791][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.792][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.794][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:11.795][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:11.796][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.797][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:53:11.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:11.799][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.801][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:11.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:11.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.808][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.809][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.810][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:11.811][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:11.812][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.813][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.814][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:53:11.816][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.817][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:11.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.819][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:11.820][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.822][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.824][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:11.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:11.826][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.827][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:53:11.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:11.829][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.830][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:11.831][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.832][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:11.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:11.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:11.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:11.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:11.839][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:11.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:11.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:11.843][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:11.848][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:11.849][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.868][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[2023-04-11 18:53:11.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.877][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[2023-04-11 18:53:11.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.890][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[2023-04-11 18:53:11.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:11.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:11.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:11.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:11.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:11.928][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:53:11.933][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:53:11.934][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:53:11.935][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:53:11.937][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:53:11.938][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:11.939][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:11.941][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:11.942][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:53:11.943][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:11.945][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:11.946][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:53:11.947][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:11.948][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:11.950][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:53:11.951][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:11.952][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:53:11.954][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:53:11.955][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:53:11.956][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:53:11.957][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:53:11.959][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:53:11.960][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:53:11.961][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:53:11.963][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:53:11.964][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:53:11.965][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:53:11.967][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:53:11.968][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:53:11.970][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:53:11.977][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:53:11.978][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:53:11.980][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:53:11.981][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:53:11.982][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:53:11.984][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:53:11.985][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:53:11.986][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:53:11.988][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:53:11.989][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:53:11.990][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:53:11.991][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:53:11.993][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:53:11.994][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:53:11.995][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:53:11.997][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:53:11.998][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:53:11.999][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:53:12.000][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:53:12.002][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:53:12.003][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:53:12.004][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:53:12.005][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:53:12.007][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:53:12.008][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:53:12.009][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:53:12.011][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:53:12.012][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:53:12.013][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:53:12.015][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:53:12.016][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:53:12.017][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:53:12.018][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:53:12.020][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:53:12.021][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:53:12.022][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:53:12.024][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:53:12.025][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:53:12.026][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:53:12.028][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:53:12.029][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:53:12.030][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:53:12.031][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:53:12.033][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:53:12.034][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:53:12.035][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:53:12.037][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:53:12.038][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:53:12.039][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:53:12.041][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:53:12.042][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:53:12.043][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:53:12.045][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:53:12.050][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:53:12.052][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:12.055][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:12.056][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.058][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.058][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[2023-04-11 18:53:12.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.092][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[2023-04-11 18:53:12.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.104][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[2023-04-11 18:53:12.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.122][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.DEBUG[2023-04-11 18:53:12.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.128][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[2023-04-11 18:53:12.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.153][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[2023-04-11 18:53:12.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.159][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[2023-04-11 18:53:12.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.165][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[2023-04-11 18:53:12.167][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:12.176][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-11 18:53:12.178][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.179][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.180][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.181][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:12.182][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.183][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.184][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.185][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-11 18:53:12.186][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:53:12.187][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:12.188][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.189][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-11 18:53:12.190][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-11 18:53:12.191][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-11 18:53:12.192][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.193][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:12.193][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:12.193][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:12.194][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:53:12.195][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.197][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:12.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.200][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.201][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:12.201][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-11 18:53:12.202][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.204][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.205][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-11 18:53:12.205][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-11 18:53:12.218][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:53:12.220][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:12.222][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-11 18:53:12.223][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:53:12.224][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:53:12.226][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:53:12.252][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-11 18:53:12.254][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-11 18:53:12.259][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-11 18:53:12.263][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-11 18:53:12.268][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.269][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.271][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-11 18:53:12.272][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-11 18:53:12.290][biodb::testThat]
biodb.INFO [2023-04-11 18:53:12.291][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-11 18:53:12.292][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:12.293][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:12.297][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-04-11 18:53:12.302][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:12.306][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:12.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:12.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:12.346][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.347][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.349][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.349][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.370][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.372][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.373][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.374][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.402][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.410][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.413][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.422][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:12.423][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:12.424][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.425][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:12.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:12.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.434][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.435][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.437][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.445][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.446][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.447][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.448][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.457][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:12.458][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.460][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.461][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:12.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.468][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.469][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.471][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.479][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.481][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.481][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.482][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:12.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.494][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.495][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:12.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.502][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:12.503][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:12.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.504][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.506][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:12.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:12.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:12.598][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-04-11 18:53:12.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:12.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:12.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:12.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:12.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:12.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:12.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:12.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:12.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.658][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:12.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:12.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:12.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:12.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.770][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.771][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.796][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.799][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.822][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.824][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.825][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:12.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:12.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.844][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.848][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.849][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.850][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.851][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:12.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:12.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.875][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.876][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.878][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:12.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.901][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.902][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.904][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:12.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.915][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.919][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.923][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.927][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.928][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.929][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.930][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:12.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.974][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.982][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.983][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.985][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:12.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.997][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.001][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.005][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.009][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.010][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.011][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.012][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.023][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.028][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.036][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.037][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.038][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.039][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.063][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.064][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.065][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.093][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.105][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.106][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.108][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.113][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:13.114][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:13.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.116][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.121][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.122][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.124][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.129][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.130][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.132][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.137][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.139][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.140][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.146][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.147][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.148][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.149][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.154][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.155][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.157][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.162][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.164][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.165][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.170][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-11 18:53:13.172][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:13.173][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.174][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.184][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.186][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.187][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.188][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.194][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.196][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:13.203][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.204][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-11 18:53:13.205][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.206][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:13.219][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-04-11 18:53:13.227][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:13.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-04-11 18:53:13.233][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:13.235][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-04-11 18:53:13.236][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:13.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:13.283][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:13.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:13.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:13.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:13.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:13.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:13.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:13.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:13.297][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.299][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.300][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.323][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:13.325][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:13.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.326][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.328][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:13.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:13.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.335][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.336][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.337][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.338][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.339][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.345][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.346][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.347][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.348][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.356][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.357][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.358][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.359][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.367][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.368][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.370][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.371][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.377][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:13.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.380][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.382][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:13.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.388][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.389][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.390][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.391][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.405][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.406][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.406][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.407][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.415][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:13.416][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:13.417][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.418][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.419][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:13.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:13.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.426][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.427][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.428][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:13.477][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-04-11 18:53:13.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-11 18:53:13.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-11 18:53:13.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-11 18:53:13.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-11 18:53:13.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-11 18:53:13.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-11 18:53:13.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:13.495][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.496][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-11 18:53:13.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.497][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:13.500][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.501][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.502][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.503][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:13.504][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-04-11 18:53:13.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.537][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:13.542][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-04-11 18:53:13.554][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-11 18:53:13.573][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:13.587][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-11 18:53:13.588][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:13.595][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-11 18:53:13.615][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:53:13.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:13.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:13.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:13.623][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-11 18:53:13.625][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-04-11 18:53:13.638][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.639][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.641][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.642][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.643][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.643][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.644][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:13.646][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.647][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-11 18:53:13.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.649][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:13.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:13.744][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[2023-04-11 18:53:13.747][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:13.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:13.749][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:13.750][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-04-11 18:53:13.765][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.766][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-11 18:53:13.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.773][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:13.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:13.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.832][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:13.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:13.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:13.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.879][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:13.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.890][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:13.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:13.896][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.897][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-11 18:53:13.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.899][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.904][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.905][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-11 18:53:13.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.907][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.912][biodb::testThat]
biodb.INFO [2023-04-11 18:53:13.913][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-11 18:53:13.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:13.915][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:13.918][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-04-11 18:53:14.943][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-04-11 18:53:16.454][biodb::testThat]
biodb.INFO [2023-04-11 18:53:16.456][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-11 18:53:16.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:16.460][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:17.016][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[2023-04-11 18:53:17.853][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:17.855][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:17.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.859][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.860][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:17.862][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:17.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.865][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:17.868][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.869][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-04-11 18:53:17.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:17.872][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:17.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:17.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:17.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:17.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:17.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:17.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:17.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:18.042][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[2023-04-11 18:53:18.046][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:18.047][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:18.049][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:18.050][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-11 18:53:18.151][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[2023-04-11 18:53:18.156][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:18.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:18.159][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:18.161][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-04-11 18:53:18.179][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:18.277][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[2023-04-11 18:53:18.281][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:18.283][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-11 18:53:18.284][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:18.286][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-11 18:53:18.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:18.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.299][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[2023-04-11 18:53:18.300][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-04-11 18:53:18.345][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:18.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-04-11 18:53:18.349][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:18.350][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:18.351][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:18.352][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:18.354][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:18.355][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:18.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:18.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.370][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-04-11 18:53:18.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:18.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:18.375][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-04-11 18:53:18.906][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-04-11 18:53:19.409][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:19.416][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-04-11 18:53:19.437][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-04-11 18:53:19.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-04-11 18:53:19.450][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:19.469][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:19.470][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:19.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:19.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:19.483][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.484][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.486][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.494][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:19.495][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:19.496][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.497][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.498][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:19.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:19.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.505][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:19.506][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:19.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.507][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.509][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:19.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:19.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.515][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:19.516][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:19.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.518][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:19.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:19.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.526][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.527][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.529][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.536][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:19.537][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:19.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.539][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.540][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:19.541][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.543][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.544][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:19.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.558][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.561][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.568][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:19.569][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:19.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.571][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:19.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:19.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.579][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:19.580][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:19.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.581][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:19.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:19.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.589][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:19.590][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:19.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.592][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:19.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:19.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:19.640][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-04-11 18:53:19.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:19.662][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[2023-04-11 18:53:19.665][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:19.666][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-11 18:53:19.667][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:19.669][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-11 18:53:19.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:19.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.694][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.TRACE[2023-04-11 18:53:19.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:19.707][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:53:19.710][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:19.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-11 18:53:19.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:19.720][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-11 18:53:19.760][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[2023-04-11 18:53:19.763][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:19.765][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:19.766][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:19.767][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-11 18:53:19.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:19.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:19.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:19.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:19.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:19.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.817][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[2023-04-11 18:53:19.818][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-04-11 18:53:19.819][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:19.820][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-04-11 18:53:19.821][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:19.822][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:19.824][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:19.825][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:19.826][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:19.826][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:19.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:19.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.851][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-04-11 18:53:19.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:19.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:19.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-04-11 18:53:20.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-04-11 18:53:20.915][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:20.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-04-11 18:53:20.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-04-11 18:53:20.942][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-04-11 18:53:20.946][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:20.964][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:20.965][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:20.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:20.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:20.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:20.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:20.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:20.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:20.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:20.979][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.982][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.990][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:20.991][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:20.992][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.993][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.994][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.995][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.997][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.998][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.999][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:21.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.001][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:21.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:21.004][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.005][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.006][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:21.007][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:21.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.009][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.010][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:21.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.013][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.014][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:21.015][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:21.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.017][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.018][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:21.019][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:21.020][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.021][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:21.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:21.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.029][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:21.030][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:21.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.032][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.033][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:21.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:21.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.047][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:21.048][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:21.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.050][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:21.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:21.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:21.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:21.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:21.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:21.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:21.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:21.094][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-04-11 18:53:21.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:21.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:21.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:21.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:21.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:21.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:21.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:21.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:21.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:21.127][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-04-11 18:53:21.128][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:21.129][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-04-11 18:53:21.130][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:21.132][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:21.133][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:21.134][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:21.135][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:21.135][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:21.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:21.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:21.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:21.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:21.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:21.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:21.148][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[2023-04-11 18:53:21.149][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-04-11 18:53:21.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:21.153][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:21.154][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-04-11 18:53:21.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-04-11 18:53:23.779][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:23.797][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-04-11 18:53:23.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-04-11 18:53:23.868][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-04-11 18:53:23.873][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:23.894][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:23.895][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:23.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:23.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:23.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:23.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:23.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:23.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:23.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:23.911][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:23.912][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:23.913][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.914][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:23.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:23.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.922][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:23.923][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:23.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.925][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.927][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:23.928][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:23.929][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.930][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.931][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:23.933][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:23.934][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.935][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.936][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:23.937][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:23.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.939][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:23.942][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:23.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.944][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.945][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:23.946][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:23.947][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.948][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.949][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:23.950][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:23.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.954][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:23.955][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:23.956][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.957][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:23.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:23.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.966][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:23.967][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:23.968][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.969][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:23.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:23.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.977][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:23.978][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:23.979][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.980][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:23.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:23.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:23.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:23.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:23.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:23.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:23.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:23.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:23.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:24.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:24.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:24.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:24.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:24.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:24.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:24.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:24.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:24.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:24.023][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-04-11 18:53:24.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:24.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:24.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:24.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:24.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:24.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:24.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:24.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:24.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:24.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:24.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:24.060][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-04-11 18:53:24.061][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:24.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-04-11 18:53:24.064][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:24.065][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:24.066][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:24.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:24.068][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:24.069][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:24.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:24.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:24.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:24.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:24.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:24.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:24.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:24.083][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-04-11 18:53:24.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:24.086][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:24.088][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-04-11 18:53:24.607][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-04-11 18:53:25.210][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:25.223][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-04-11 18:53:25.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-04-11 18:53:25.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-04-11 18:53:25.265][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:25.296][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:25.298][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:25.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:25.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:25.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:25.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:25.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:25.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:25.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:25.315][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.316][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.318][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.327][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:25.328][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:25.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.331][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:25.332][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:25.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.334][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.335][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:25.345][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:25.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.347][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:25.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:25.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.351][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.352][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:25.353][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:25.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.355][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.356][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:25.357][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.358][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.359][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.360][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:25.361][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:25.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.363][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.364][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:25.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:25.366][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.367][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:25.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:25.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.376][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:25.377][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:25.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.379][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.380][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:25.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.387][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:25.388][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:25.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.390][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:25.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:25.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:25.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:25.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:25.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:25.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:25.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:25.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:25.434][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-04-11 18:53:25.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:25.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:25.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:25.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:25.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:25.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:25.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:25.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:25.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:25.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:25.466][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[2023-04-11 18:53:25.467][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-04-11 18:53:25.468][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:25.470][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-04-11 18:53:25.471][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:25.472][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:25.473][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:25.474][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:25.475][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:25.476][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:25.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:25.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:25.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:25.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:25.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:25.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:25.489][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.DEBUG[2023-04-11 18:53:25.490][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-04-11 18:53:25.493][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:25.494][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:25.496][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-04-11 18:53:26.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-04-11 18:53:26.760][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:26.771][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-04-11 18:53:26.787][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-04-11 18:53:26.803][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-04-11 18:53:26.809][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:26.839][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:26.841][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:26.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:26.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:26.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:26.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:26.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:26.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:26.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:26.862][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:26.863][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:26.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.866][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:26.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:26.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.878][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:26.880][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:26.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.882][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.884][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:26.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.894][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:26.896][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:26.897][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.898][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:26.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:26.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:26.910][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:26.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.912][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:26.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:26.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.920][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:26.921][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:26.922][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.923][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:26.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:26.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.931][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:26.932][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:26.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.934][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.936][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:26.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:26.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.943][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:26.944][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:26.945][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.946][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.948][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:26.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:26.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:26.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:26.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.958][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.974][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:26.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:26.977][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.978][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:26.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:26.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.987][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:26.988][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:26.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.990][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.991][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:26.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:26.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:26.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:26.999][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:27.000][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:27.001][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.002][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.003][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:27.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:27.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:27.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:27.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:27.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:27.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:27.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:27.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:27.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:27.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:27.056][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-04-11 18:53:27.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:27.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:27.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:27.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:27.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:27.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:27.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:27.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:27.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:27.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:27.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:27.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:27.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:27.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:27.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:27.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:27.081][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-04-11 18:53:27.082][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:27.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-04-11 18:53:27.085][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:27.086][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:27.087][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:27.088][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:27.089][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:27.090][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:27.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:27.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:27.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:27.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:27.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:27.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:27.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:27.105][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-04-11 18:53:27.107][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:27.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:27.110][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-04-11 18:53:27.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-04-11 18:53:28.620][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:28.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-04-11 18:53:28.639][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-04-11 18:53:28.649][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-04-11 18:53:28.653][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:28.673][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:28.675][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:28.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:28.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:28.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:28.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:28.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:28.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:28.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:28.690][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.691][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.692][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.693][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.701][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:28.702][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:28.703][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.704][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.706][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:28.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:28.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.713][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:28.714][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:28.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.716][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:28.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:28.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.725][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:28.726][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:28.727][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.728][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:28.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:28.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.737][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:28.738][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:28.739][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.740][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:28.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:28.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.749][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:28.750][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:28.751][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.752][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.753][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.760][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:28.762][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.763][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.764][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.765][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:28.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:28.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:28.775][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.775][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:28.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.784][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:28.785][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:28.786][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.786][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:28.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:28.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.795][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:28.796][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:28.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.798][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.799][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:28.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:28.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.812][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:28.813][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:28.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.815][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.816][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:28.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:28.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:28.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:28.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:28.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:28.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:28.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:28.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:28.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:28.867][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-04-11 18:53:28.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:28.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:28.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:28.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:28.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:28.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:28.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:28.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:28.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:28.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:28.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:28.890][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-04-11 18:53:28.891][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:28.893][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-04-11 18:53:28.894][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:28.895][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:28.896][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:28.897][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:28.898][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:28.899][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:28.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:28.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:28.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:28.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:28.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:28.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:28.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:28.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-04-11 18:53:28.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:28.917][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:28.918][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-04-11 18:53:29.502][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-04-11 18:53:30.159][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:30.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-04-11 18:53:30.187][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-04-11 18:53:30.214][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-04-11 18:53:30.221][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:30.250][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:30.252][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:30.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:30.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:30.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:30.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:30.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:30.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:30.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:30.266][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.268][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.269][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.277][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:30.278][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:30.279][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.280][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.281][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:30.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.288][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:30.289][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:30.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.290][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:30.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:30.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.298][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:30.299][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:30.300][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.301][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:30.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:30.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.309][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:30.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:30.311][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.311][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:30.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:30.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.319][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:30.320][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:30.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.322][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.323][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:30.324][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.326][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:30.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.334][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:30.335][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:30.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.336][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:30.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:30.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.344][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:30.345][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:30.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.347][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:30.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:30.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.355][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:30.356][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:30.357][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.357][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.359][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:30.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:30.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.365][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:30.366][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:30.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.368][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.369][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:30.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:30.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:30.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:30.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:30.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:30.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:30.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:30.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:30.447][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-04-11 18:53:30.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:30.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:30.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:30.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:30.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:30.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:30.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:30.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:30.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:30.470][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-04-11 18:53:30.471][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:30.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-04-11 18:53:30.473][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:30.474][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:30.475][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:30.476][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:30.477][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:30.478][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:30.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:30.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:30.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:30.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:30.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:30.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:30.491][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[2023-04-11 18:53:30.492][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-04-11 18:53:30.494][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:30.495][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:30.497][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-04-11 18:53:30.999][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-04-11 18:53:31.523][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:31.531][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-04-11 18:53:31.542][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-04-11 18:53:31.553][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-04-11 18:53:31.557][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:31.585][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:31.586][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:31.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:31.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:31.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:31.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:31.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:31.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:31.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:31.600][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.602][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.603][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.612][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:31.613][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:31.614][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.615][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.616][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:31.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:31.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.623][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:31.624][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:31.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.626][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:31.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:31.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.635][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:31.636][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:31.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.638][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:31.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:31.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.646][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:31.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:31.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.649][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:31.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:31.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:31.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:31.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.660][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.661][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:31.662][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.663][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.664][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.665][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.672][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:31.673][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:31.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.674][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:31.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:31.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.682][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:31.683][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:31.684][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.685][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:31.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:31.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.693][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:31.694][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:31.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.696][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.697][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:31.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.704][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:31.705][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:31.706][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.707][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.708][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:31.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:31.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:31.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:31.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:31.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:31.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:31.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:31.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:31.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:31.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:31.757][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-04-11 18:53:31.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:31.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:31.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:31.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:31.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:31.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:31.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:31.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:31.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:31.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:31.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:31.786][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-04-11 18:53:31.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:31.788][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-04-11 18:53:31.790][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:31.791][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:31.792][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:31.793][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:31.794][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:31.795][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:31.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:31.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:31.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:31.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:31.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:31.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:31.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:31.809][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-04-11 18:53:31.812][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:31.813][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:31.814][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-04-11 18:53:32.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-04-11 18:53:32.867][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:32.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-04-11 18:53:32.894][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-04-11 18:53:32.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-04-11 18:53:32.913][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:32.933][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:32.934][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:32.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:32.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:32.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:32.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:32.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:32.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:32.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:32.948][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:32.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:32.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.951][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:32.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:32.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.959][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:32.960][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:32.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.968][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.973][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:32.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:32.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.980][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:32.982][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:32.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.983][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:32.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:32.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.991][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:32.992][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:32.993][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.994][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:32.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:32.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:32.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:32.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:33.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:33.004][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.005][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:33.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:33.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.013][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:33.014][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:33.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.016][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.017][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:33.018][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.020][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.021][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:33.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.028][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:33.029][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:33.030][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.031][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:33.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:33.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.039][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:33.040][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:33.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.041][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:33.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:33.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.049][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:33.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:33.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.052][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.053][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:33.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:33.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.060][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:33.061][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:33.062][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.063][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.064][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:33.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:33.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:33.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:33.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:33.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:33.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:33.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:33.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:33.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:33.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:33.113][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-04-11 18:53:33.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:33.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:33.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:33.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:33.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:33.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:33.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:33.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:33.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:33.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.137][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-04-11 18:53:33.138][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:33.139][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-04-11 18:53:33.140][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:33.141][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:33.142][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:33.143][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:33.149][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:33.150][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:33.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:33.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:33.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:33.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:33.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:33.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.164][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-04-11 18:53:33.167][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:33.168][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:33.169][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-04-11 18:53:33.671][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-04-11 18:53:34.196][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:34.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-04-11 18:53:34.227][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-04-11 18:53:34.245][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-04-11 18:53:34.251][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:34.286][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:34.287][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:34.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:34.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:34.304][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.305][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.307][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.316][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:34.317][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:34.318][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.319][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.320][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:34.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.328][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:34.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:34.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.331][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:34.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.340][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:34.341][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:34.342][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.343][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:34.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:34.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.352][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:34.353][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:34.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.371][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:34.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:34.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.380][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:34.381][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:34.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.383][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.385][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:34.386][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.387][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.388][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.389][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:34.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.397][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:34.398][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:34.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.400][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:34.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:34.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.408][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.410][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.411][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.419][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:34.420][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:34.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.422][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.423][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:34.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:34.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.430][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:34.431][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:34.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.433][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.434][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:34.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:34.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:34.482][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-04-11 18:53:34.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:34.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:34.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:34.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.506][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-04-11 18:53:34.507][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:34.509][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-04-11 18:53:34.510][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:34.511][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:34.512][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:34.513][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:34.514][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:34.515][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:34.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:34.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.528][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[2023-04-11 18:53:34.529][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-04-11 18:53:34.532][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:34.533][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:34.534][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-04-11 18:53:35.063][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-04-11 18:53:35.608][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:35.616][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-04-11 18:53:35.626][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-04-11 18:53:35.636][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-04-11 18:53:35.640][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:35.659][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:35.661][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:35.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:35.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:35.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:35.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:35.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:35.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:35.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:35.675][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.676][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.678][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.685][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:35.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:35.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.688][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.689][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:35.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:35.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.696][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.697][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.698][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.699][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.707][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:35.708][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:35.709][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.710][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:35.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:35.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.718][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:35.719][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:35.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.721][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:35.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:35.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.729][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:35.730][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:35.731][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.732][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.733][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:35.734][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.736][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:35.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.744][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.745][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.746][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.746][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.763][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.766][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.774][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:35.775][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:35.776][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.777][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.778][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:35.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:35.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.785][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:35.786][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:35.787][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.788][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.789][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:35.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:35.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:35.840][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-04-11 18:53:35.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:35.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:35.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:35.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:35.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:35.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:35.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:35.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:35.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:35.864][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-04-11 18:53:35.865][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:35.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-04-11 18:53:35.868][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:35.869][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:35.870][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:35.871][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:35.872][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:35.873][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:35.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:35.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:35.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:35.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:35.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:35.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:35.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:35.888][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-04-11 18:53:35.891][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:35.892][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:35.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-04-11 18:53:36.389][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-04-11 18:53:36.903][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:36.911][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-04-11 18:53:36.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-04-11 18:53:36.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-04-11 18:53:36.937][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:36.956][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:36.958][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:36.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:36.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:36.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:36.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:36.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:36.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:36.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:36.974][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:36.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:36.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:36.977][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:36.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:36.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:36.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:36.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:36.987][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:36.988][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:36.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:36.990][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:36.991][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:36.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:36.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:36.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:36.998][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:36.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:37.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.001][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:37.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:37.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.009][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:37.010][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:37.011][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.012][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.013][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:37.014][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:37.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.016][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.017][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:37.018][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:37.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.020][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.022][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:37.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.024][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.025][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.026][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:37.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:37.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:37.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.036][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:37.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:37.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.044][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:37.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:37.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.047][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:37.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:37.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.056][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:37.057][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:37.058][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.059][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.060][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:37.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.067][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:37.068][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:37.069][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.070][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:37.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:37.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:37.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:37.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:37.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:37.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:37.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:37.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:37.122][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-04-11 18:53:37.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:37.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:37.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:37.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:37.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:37.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:37.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:37.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:37.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:37.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:37.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:37.146][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-04-11 18:53:37.147][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:37.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-04-11 18:53:37.150][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:37.151][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:37.152][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:37.153][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:37.154][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:37.155][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:37.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:37.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:37.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:37.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:37.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:37.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:37.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:37.169][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-04-11 18:53:37.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:37.173][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:37.174][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-04-11 18:53:37.877][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-04-11 18:53:38.429][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:38.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-04-11 18:53:38.458][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-04-11 18:53:38.474][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-04-11 18:53:38.481][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:38.525][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:38.527][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:38.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:38.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:38.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:38.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:38.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:38.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:38.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:38.549][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.551][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.552][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.553][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.561][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:38.562][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:38.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.564][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.565][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:38.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:38.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.572][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:38.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:38.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.575][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.576][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:38.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:38.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:38.584][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:38.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.586][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.587][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:38.588][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:38.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.590][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.591][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:38.592][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:38.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.594][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.595][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:38.596][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.598][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.599][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:38.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:38.607][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:38.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.609][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:38.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:38.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.617][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:38.618][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:38.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.620][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:38.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:38.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.629][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:38.630][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:38.631][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.632][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.633][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:38.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:38.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.640][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:38.641][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:38.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.643][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:38.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:38.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:38.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:38.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:38.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:38.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:38.687][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-04-11 18:53:38.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:38.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:38.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:38.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:38.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:38.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:38.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:38.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:38.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:38.718][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-04-11 18:53:38.719][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:38.721][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-04-11 18:53:38.722][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:38.723][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:38.725][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:38.726][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:38.727][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:38.728][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:38.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:38.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:38.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:38.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:38.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:38.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:38.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:38.742][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-04-11 18:53:38.745][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:38.746][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:38.748][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-04-11 18:53:39.324][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-04-11 18:53:39.992][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-04-11 18:53:40.002][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-04-11 18:53:40.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-04-11 18:53:40.030][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-04-11 18:53:40.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-04-11 18:53:40.048][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:40.077][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:40.079][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:40.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:40.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:40.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:40.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:40.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:40.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:40.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:40.101][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.106][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.116][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:40.117][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:40.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.119][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:40.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.129][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:40.130][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:40.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.133][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:40.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:40.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.167][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:40.168][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:40.170][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.171][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:40.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:40.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:40.182][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:40.184][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.185][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:40.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:40.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.195][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:40.196][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:40.198][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.199][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.200][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:40.201][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.202][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.203][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.205][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:40.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.213][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:40.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:40.216][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.217][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.226][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:40.227][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:40.228][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.229][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:40.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:40.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.239][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:40.241][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:40.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.244][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.246][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:40.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:40.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.254][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:40.256][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:40.257][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.258][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.259][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:40.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:40.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:40.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:40.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:40.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:40.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:40.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:40.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:40.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:40.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:40.319][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-04-11 18:53:40.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:40.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:40.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:40.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:40.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:40.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:40.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:40.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:40.351][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-04-11 18:53:40.352][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:40.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-04-11 18:53:40.356][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:40.357][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:40.358][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:40.360][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:40.361][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:40.362][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:40.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:40.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:40.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:40.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:40.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:40.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:40.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:40.387][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-04-11 18:53:40.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:40.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:40.393][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-04-11 18:53:45.953][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-04-11 18:53:46.515][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-04-11 18:53:46.520][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-04-11 18:53:46.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-04-11 18:53:46.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-04-11 18:53:46.547][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-04-11 18:53:46.555][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:46.582][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:46.584][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:46.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:46.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:46.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:46.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:46.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:46.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:46.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:46.601][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.602][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.604][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.613][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:46.615][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:46.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.617][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:46.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:46.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.626][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:46.627][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:46.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.629][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.630][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:46.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:46.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:46.639][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:46.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.641][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:46.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:46.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.649][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:46.650][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:46.651][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.652][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:46.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:46.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.680][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:46.681][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:46.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.684][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.685][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:46.687][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.688][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.689][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.690][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:46.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:46.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:46.699][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.700][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:46.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:46.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.709][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:46.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:46.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.712][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:46.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:46.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.720][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:46.721][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:46.722][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.723][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:46.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:46.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.732][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:46.733][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:46.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.735][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.736][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:46.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:46.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:46.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:46.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:46.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:46.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:46.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:46.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:46.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:46.788][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-04-11 18:53:46.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:46.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:46.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:46.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:46.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:46.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:46.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:46.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:46.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:46.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:46.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:46.811][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-04-11 18:53:46.812][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:46.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-04-11 18:53:46.815][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:46.816][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:46.817][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:46.819][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:46.820][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:46.821][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:46.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:46.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:46.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:46.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:46.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:46.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:46.833][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[2023-04-11 18:53:46.835][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-04-11 18:53:46.837][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:46.838][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:46.840][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-04-11 18:53:47.362][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-04-11 18:53:47.869][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:47.876][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-04-11 18:53:47.887][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-04-11 18:53:47.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-04-11 18:53:47.900][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:47.919][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:47.921][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:47.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:47.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:47.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:47.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:47.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:47.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:47.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:47.936][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:47.937][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:47.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.938][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:47.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:47.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.946][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:47.947][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:47.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.949][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.951][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:47.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:47.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.957][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:47.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:47.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.960][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:47.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:47.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.968][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:47.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:47.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.971][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:47.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:47.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.979][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:47.980][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:47.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.982][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:47.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:47.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.990][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:47.991][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:47.992][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.993][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.994][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:47.995][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:47.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:47.997][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:47.998][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:47.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.006][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:48.007][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:48.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.009][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:48.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:48.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.021][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:48.025][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:48.026][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.027][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:48.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:48.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.035][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:48.036][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:48.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.038][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.039][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:48.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:48.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.046][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:48.047][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:48.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.049][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.050][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:48.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:48.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:48.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:48.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:48.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:48.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:48.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:48.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:48.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:48.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:48.099][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-04-11 18:53:48.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:48.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:48.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:48.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:48.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:48.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:48.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:48.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:48.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:48.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:48.122][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.DEBUG[2023-04-11 18:53:48.123][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-04-11 18:53:48.124][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:48.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-04-11 18:53:48.127][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:48.128][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:48.129][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:48.130][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:48.131][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:48.132][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:48.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:48.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:48.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:48.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:48.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:48.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:48.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:48.145][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-04-11 18:53:48.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:48.149][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:48.150][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-04-11 18:53:48.646][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-04-11 18:53:49.183][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:49.197][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-04-11 18:53:49.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-04-11 18:53:49.226][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-04-11 18:53:49.230][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:49.249][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:49.251][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:49.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:49.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:49.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:49.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:49.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:49.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:49.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:49.266][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.268][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.269][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.277][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:49.279][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:49.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.281][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.282][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:49.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:49.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.290][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:49.291][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:49.292][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.293][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:49.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:49.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.301][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:49.302][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:49.303][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.304][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.312][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:49.313][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:49.314][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.315][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:49.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:49.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.323][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:49.324][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:49.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.326][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.328][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:49.329][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.331][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.332][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:49.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.339][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:49.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:49.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:49.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:49.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.351][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:49.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:49.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.354][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:49.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:49.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.362][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:49.363][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:49.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.365][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:49.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:49.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.374][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:49.375][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:49.376][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.377][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.384][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:49.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:49.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:49.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:49.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:49.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:49.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:49.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:49.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:49.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:49.436][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-04-11 18:53:49.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:49.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:49.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:49.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:49.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:49.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:49.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:49.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:49.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:49.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:49.461][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-04-11 18:53:49.462][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:49.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-04-11 18:53:49.472][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:49.474][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:49.476][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:49.478][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:49.480][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:49.481][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:49.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:49.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:49.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:49.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:49.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:49.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:49.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:49.504][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-04-11 18:53:49.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:49.509][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:49.511][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-04-11 18:53:50.105][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-04-11 18:53:50.631][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:50.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-04-11 18:53:50.652][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-04-11 18:53:50.684][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-04-11 18:53:50.689][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:50.710][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:50.712][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:50.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:50.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:50.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:50.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:50.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:50.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:50.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:50.728][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.729][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.730][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.731][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.740][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:50.741][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:50.742][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.743][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.744][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:50.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:50.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.751][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:50.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:50.753][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.754][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:50.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.764][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:50.765][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:50.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.767][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:50.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:50.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.775][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:50.776][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:50.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.778][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:50.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:50.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:50.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:50.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.789][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.790][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:50.791][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.792][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.793][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.794][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:50.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.801][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:50.802][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:50.803][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.804][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:50.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:50.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.812][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:50.813][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:50.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.815][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:50.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.823][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:50.825][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:50.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.826][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.828][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:50.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:50.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.835][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:50.836][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:50.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.838][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:50.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:50.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:50.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:50.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:50.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:50.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:50.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:50.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:50.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:50.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:50.899][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-04-11 18:53:50.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:50.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:50.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:50.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:50.947][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[2023-04-11 18:53:50.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:50.952][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:50.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:53:51.629][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:53:52.258][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:52.264][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-04-11 18:53:52.275][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-04-11 18:53:52.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:52.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:52.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:52.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:52.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:52.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:52.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:52.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:52.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:52.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:52.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:52.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:52.851][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:53:52.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:52.856][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:52.858][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:53:53.399][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:53:53.933][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:53.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-04-11 18:53:53.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-04-11 18:53:53.966][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[2023-04-11 18:53:53.971][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:53.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:53.975][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:53:54.476][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:53:55.000][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:55.007][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-04-11 18:53:55.019][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-04-11 18:53:55.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:55.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:55.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:55.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:55.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:55.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:55.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:55.059][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-04-11 18:53:55.060][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:55.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-04-11 18:53:55.063][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:55.064][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:55.066][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:55.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:55.068][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:55.069][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:55.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:55.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:55.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:55.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:55.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:55.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:55.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:55.084][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-04-11 18:53:55.086][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:55.087][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:55.093][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-04-11 18:53:55.595][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-04-11 18:53:56.213][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:56.221][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-04-11 18:53:56.234][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-04-11 18:53:56.245][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-04-11 18:53:56.250][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:56.272][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:56.274][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:56.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:56.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:56.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:56.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:56.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:56.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:56.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:56.292][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.294][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.295][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.296][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.305][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:56.306][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:56.307][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.308][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.310][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:56.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:56.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.318][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:56.319][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:56.320][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.321][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:56.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:56.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.348][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:56.349][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:56.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.351][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:56.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:56.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.360][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:56.361][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:56.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.363][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:56.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:56.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.371][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:56.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:56.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.375][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.376][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:56.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:56.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.383][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:56.384][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:56.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.386][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.387][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:56.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:56.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.394][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.396][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.397][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.397][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.406][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:56.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:56.408][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.409][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:56.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:56.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.417][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:56.418][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:56.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.420][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.421][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:56.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.429][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:56.430][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:56.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.432][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:56.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:56.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:56.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:56.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:56.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:56.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:56.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:56.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:56.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:56.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:56.485][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-04-11 18:53:56.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:56.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:56.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:56.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:56.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:56.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:56.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:56.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:56.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:56.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:56.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:56.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:56.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:56.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:56.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:56.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:56.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:56.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:56.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:56.539][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-04-11 18:53:56.540][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:56.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-04-11 18:53:56.542][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:56.543][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:56.544][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:56.545][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:53:56.546][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:53:56.547][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:53:56.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:56.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:56.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:56.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:56.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:56.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:56.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:56.562][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-04-11 18:53:56.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:56.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:56.567][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-04-11 18:53:57.067][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-04-11 18:53:57.570][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:57.577][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-04-11 18:53:57.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-04-11 18:53:57.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-04-11 18:53:57.602][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:53:57.620][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:57.621][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:53:57.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:57.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:57.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:57.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:57.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:57.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:57.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:57.635][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.638][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.646][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:57.647][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:57.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.649][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:53:57.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:53:57.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.657][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:57.658][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:57.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.670][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:57.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:57.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:57.681][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:57.682][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.683][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:57.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:57.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.691][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:57.692][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:57.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.693][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:57.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:57.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.702][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:57.703][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:57.704][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.704][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.706][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:57.707][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:57.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.709][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.710][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:53:57.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:57.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.717][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.718][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.719][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.727][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:57.728][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:57.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.730][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:57.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:57.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.738][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:57.739][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:57.740][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.741][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.742][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:53:57.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:53:57.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.749][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:57.750][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:57.751][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.752][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.753][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:57.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:57.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:57.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:57.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:57.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:57.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:57.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:57.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:57.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:57.808][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-04-11 18:53:57.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:57.891][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:53:57.895][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:57.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:57.898][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:57.899][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-11 18:53:57.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:57.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:57.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:57.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:57.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:57.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:57.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:57.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:57.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:57.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:57.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:57.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:57.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:57.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:57.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:57.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:57.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:57.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:57.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:57.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:57.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:57.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:57.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:57.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:57.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:57.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:57.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:53:58.439][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:58.441][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-11 18:53:58.442][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:58.443][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-11 18:53:58.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:58.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:58.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:58.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:58.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:58.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:58.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:58.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:58.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:58.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.944][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:53:58.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:53:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:58.966][biodb::testThat]
biodb.INFO [2023-04-11 18:53:58.967][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-11 18:53:58.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:58.969][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:58.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:58.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:58.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:58.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:59.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:59.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:59.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:59.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:59.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:59.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:59.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:59.049][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:53:59.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:59.053][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:59.055][private$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[2023-04-11 18:53:59.572][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[2023-04-11 18:54:00.081][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:00.095][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-04-11 18:54:00.113][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-04-11 18:54:00.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:00.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:00.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:00.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:00.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:00.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:00.156][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[2023-04-11 18:54:00.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:00.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:00.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:00.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:00.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:00.171][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[2023-04-11 18:54:00.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:00.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:00.178][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:54:00.678][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:54:01.287][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:01.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-04-11 18:54:01.307][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-04-11 18:54:01.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:01.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:01.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:01.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:01.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:01.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:01.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:01.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:01.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:01.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:01.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:01.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:01.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:01.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:01.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:01.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:01.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:01.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:01.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:01.341][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:01.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:01.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:01.347][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:54:01.866][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:54:02.410][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:02.441][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-04-11 18:54:02.460][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-04-11 18:54:02.468][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:02.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:02.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:02.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:02.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:02.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:02.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:02.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.492][private$selectFields]
biodb.TRACE[2023-04-11 18:54:02.493][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:02.494][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:02.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.498][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.499][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.500][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.502][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.503][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.505][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.508][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.509][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.510][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:02.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.533][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-11 18:54:02.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:02.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:02.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:02.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:02.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:02.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:02.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:02.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.557][private$selectFields]
biodb.TRACE[2023-04-11 18:54:02.558][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:02.559][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:02.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.563][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.566][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.566][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.567][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.568][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.569][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:02.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.571][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.573][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.574][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:02.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.588][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-11 18:54:02.589][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:02.590][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:02.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:02.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:02.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:02.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:02.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:02.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:02.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:02.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:02.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:02.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:02.768][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:02.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:02.775][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:02.777][private$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[2023-04-11 18:54:03.311][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[2023-04-11 18:54:04.287][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:04.299][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-04-11 18:54:04.317][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-04-11 18:54:04.326][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[2023-04-11 18:54:04.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:04.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:04.336][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:54:04.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:54:05.412][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:05.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-04-11 18:54:05.434][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-04-11 18:54:05.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:05.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:05.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:05.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:05.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:05.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:05.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:05.562][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:05.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:05.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.608][private$selectFields]
biodb.TRACE[2023-04-11 18:54:05.608][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:05.609][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:05.610][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.614][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.618][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.619][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.620][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.621][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.622][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.624][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.625][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.638][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-11 18:54:05.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.650][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.TRACE[2023-04-11 18:54:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.699][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.700][private$selectFields]
biodb.TRACE[2023-04-11 18:54:05.701][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:05.702][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:05.703][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.704][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.705][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.706][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.707][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.708][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.709][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.711][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.712][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.722][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.723][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.724][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.725][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.726][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.727][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:05.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.741][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-11 18:54:05.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:05.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.760][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.761][private$selectFields]
biodb.TRACE[2023-04-11 18:54:05.762][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:05.763][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:05.764][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.765][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.767][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.768][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.768][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.770][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.770][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.771][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:05.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.776][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.777][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.778][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:05.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:05.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-11 18:54:05.792][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:05.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:05.801][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:05.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:05.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:05.806][biodb::testThat]
biodb.INFO [2023-04-11 18:54:05.807][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-11 18:54:05.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:05.809][biodb::testThat]
biodb.TRACE[2023-04-11 18:54:05.812][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:54:05.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:54:05.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:05.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:05.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:05.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:05.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:05.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:05.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:05.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:05.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:05.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:06.056][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.060][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-11 18:54:06.062][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.064][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-11 18:54:06.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.088][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.091][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.093][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-11 18:54:06.094][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.095][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-11 18:54:06.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.120][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-11 18:54:06.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.127][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-11 18:54:06.129][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:06.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.150][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.151][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.152][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.153][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.156][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.157][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.158][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.160][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.161][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.162][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.163][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.165][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.166][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.167][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.180][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-11 18:54:06.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.195][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.TRACE[2023-04-11 18:54:06.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.204][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.204][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.205][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.206][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.207][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.211][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.212][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.213][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.215][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.215][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.216][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.219][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.220][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.221][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.234][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-11 18:54:06.235][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:06.235][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:06.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.275][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[2023-04-11 18:54:06.311][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-04-11 18:54:06.317][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.318][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-04-11 18:54:06.321][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[2023-04-11 18:54:06.324][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.325][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-04-11 18:54:06.326][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.327][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-04-11 18:54:06.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.339][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[2023-04-11 18:54:06.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.400][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:06.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.419][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.420][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.421][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.422][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.423][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.423][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.424][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.426][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.427][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.428][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.429][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.430][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.431][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.432][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.434][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.434][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.435][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.436][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.449][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-11 18:54:06.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.471][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.472][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.473][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.473][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.474][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.477][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.478][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.481][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.482][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.484][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.487][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.488][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.489][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.501][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-11 18:54:06.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.526][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.526][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.527][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.528][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.533][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.537][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.537][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.538][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.539][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.540][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.542][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.543][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.556][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-11 18:54:06.556][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:06.557][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:06.565][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:06.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:06.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:06.570][biodb::testThat]
biodb.INFO [2023-04-11 18:54:06.571][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-11 18:54:06.572][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:06.573][biodb::testThat]
biodb.TRACE[2023-04-11 18:54:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:54:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:54:06.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:06.652][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[2023-04-11 18:54:06.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.657][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-11 18:54:06.658][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.659][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-11 18:54:06.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.685][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[2023-04-11 18:54:06.688][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-11 18:54:06.690][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.692][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-11 18:54:06.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.722][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.726][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-11 18:54:06.727][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.729][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-11 18:54:06.731][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:06.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.750][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.751][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.752][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.753][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.754][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.756][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.757][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.758][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.760][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.761][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.763][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.764][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.765][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.767][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.768][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.780][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-11 18:54:06.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.800][private$selectFields]
biodb.TRACE[2023-04-11 18:54:06.801][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:06.802][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:06.803][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.804][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.805][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.807][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.809][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.811][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.812][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.813][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:06.814][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.815][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.816][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.817][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.817][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:06.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:06.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.831][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-11 18:54:06.832][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:06.833][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:06.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:06.928][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.932][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-04-11 18:54:06.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.936][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-04-11 18:54:06.939][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:06.942][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:06.943][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-04-11 18:54:06.944][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:06.946][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-04-11 18:54:06.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:06.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:06.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:06.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:06.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:06.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:06.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:06.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:06.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:06.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:06.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:07.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:07.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:07.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:07.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:07.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:07.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:07.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:07.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:07.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:07.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:07.015][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:07.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:07.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:07.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:07.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:07.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:07.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:07.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:07.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.041][private$selectFields]
biodb.TRACE[2023-04-11 18:54:07.042][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:07.043][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:07.044][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.047][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.048][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.051][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.052][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.053][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.054][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.055][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.056][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.057][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.058][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:07.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.070][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-11 18:54:07.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:07.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:07.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:07.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:07.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:07.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:07.081][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[2023-04-11 18:54:07.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.091][private$selectFields]
biodb.TRACE[2023-04-11 18:54:07.092][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:07.092][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:07.093][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.097][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.100][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.101][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.103][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.106][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.107][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:07.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.120][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-11 18:54:07.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:07.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:07.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:07.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:07.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:07.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:07.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:07.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.140][private$selectFields]
biodb.TRACE[2023-04-11 18:54:07.141][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:07.142][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:07.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.147][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.148][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.149][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.150][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.151][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.152][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.153][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-11 18:54:07.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.157][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.158][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-11 18:54:07.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:07.171][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-11 18:54:07.172][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:07.173][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:07.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:07.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:07.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:07.204][biodb::testThat]
biodb.INFO [2023-04-11 18:54:07.205][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-11 18:54:07.206][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:07.207][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:07.209][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-11 18:54:07.210][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:54:07.211][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-11 18:54:07.213][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:54:07.214][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:54:07.215][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:54:07.216][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:54:07.217][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:54:07.218][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:54:07.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:07.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:07.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:07.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:07.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:07.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:07.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:07.231][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-04-11 18:54:07.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:07.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:07.236][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-04-11 18:54:07.746][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-04-11 18:54:08.286][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:08.294][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-04-11 18:54:08.306][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-04-11 18:54:08.316][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-04-11 18:54:08.320][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:54:08.340][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:54:08.342][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:54:08.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:08.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:08.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:08.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:08.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:08.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:08.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:08.360][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.361][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.363][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.373][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:08.374][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:08.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.376][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.377][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:08.379][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:08.380][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.381][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.382][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:08.383][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:08.384][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.385][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.387][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:08.388][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:08.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.390][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.391][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:08.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:08.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.412][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:08.413][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:08.414][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.415][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:08.418][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:08.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.419][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.421][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:08.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:08.423][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.424][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.425][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:08.426][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:08.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.428][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.430][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:08.431][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:08.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.433][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:08.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:08.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:08.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:08.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:08.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:08.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:08.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:08.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:08.477][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-04-11 18:54:08.478][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-11 18:54:08.484][biodb::testThat]
biodb.INFO [2023-04-11 18:54:08.485][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-11 18:54:08.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:08.487][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:08.496][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-04-11 18:54:08.497][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-04-11 18:54:08.499][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-04-11 18:54:08.500][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-04-11 18:54:08.501][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-04-11 18:54:08.502][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:54:08.503][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:54:08.504][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:54:08.505][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:54:08.506][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:54:08.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:08.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:08.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:08.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:08.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:08.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:08.520][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[2023-04-11 18:54:08.521][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-04-11 18:54:08.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:08.524][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:08.526][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-04-11 18:54:09.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-04-11 18:54:09.556][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:09.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-04-11 18:54:09.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-04-11 18:54:09.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:09.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:09.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:09.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:09.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:09.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:09.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:09.598][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-04-11 18:54:09.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:09.601][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:09.603][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-04-11 18:54:10.211][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-04-11 18:54:10.735][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:10.747][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-04-11 18:54:10.764][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-04-11 18:54:10.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:10.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:10.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:10.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:10.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:10.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:10.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:10.789][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-04-11 18:54:10.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:10.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:10.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-04-11 18:54:11.339][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-04-11 18:54:11.861][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:11.869][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-04-11 18:54:11.880][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-04-11 18:54:11.902][private$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[2023-04-11 18:54:11.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:54:11.926][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-04-11 18:54:11.928][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-04-11 18:54:11.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:11.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:11.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:11.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:11.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:11.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:11.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:11.943][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:11.944][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:11.945][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.946][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:11.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:11.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.955][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:11.956][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:11.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.958][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.959][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:11.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:11.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.962][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.964][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:11.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:11.966][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.967][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.968][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:11.969][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:11.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.971][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.972][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:11.973][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:11.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.975][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.976][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:11.977][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:11.978][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.979][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.980][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:11.981][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:11.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.983][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.984][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:11.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:11.986][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.987][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.988][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:11.989][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:11.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.991][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.992][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:11.993][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:11.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.995][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:11.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:11.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:11.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:11.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:12.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:12.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:12.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:12.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:12.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:12.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:12.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:12.038][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.041][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.049][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:12.050][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:12.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.052][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:12.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:12.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.060][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:12.061][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:12.062][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.063][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:12.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:12.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.071][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:12.072][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:12.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.074][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:12.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:12.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.086][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.087][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.089][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.096][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.097][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.098][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.099][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.100][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.107][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:12.108][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:12.109][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.110][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.111][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:12.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:12.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.117][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.119][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.120][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.128][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:12.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:12.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.131][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:12.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:12.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.139][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:12.140][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:12.141][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.141][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:12.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:12.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:12.150][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:12.151][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.152][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.153][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:12.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:12.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:12.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:12.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:12.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:12.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:12.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:12.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:12.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:12.201][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.202][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.204][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.212][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:12.213][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:12.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.215][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.216][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:12.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:12.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.223][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:12.224][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:12.225][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.226][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:12.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:12.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.234][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:12.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:12.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.237][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:12.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:12.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.246][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.252][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.253][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:12.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.261][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.263][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.264][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.265][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:12.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.271][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:12.272][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:12.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.274][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.275][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:12.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:12.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.282][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.283][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.283][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.284][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.293][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:12.294][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:12.294][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.295][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:12.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:12.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.304][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:12.305][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:12.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.307][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.308][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:12.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:12.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.315][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:12.316][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:12.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.318][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.319][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:12.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:12.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:12.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:12.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:12.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:12.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:12.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:12.390][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-04-11 18:54:12.391][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-11 18:54:12.392][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-11 18:54:12.403][biodb::testThat]
biodb.INFO [2023-04-11 18:54:12.404][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-11 18:54:12.405][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:12.406][biodb::testThat]
biodb.INFO [2023-04-11 18:54:12.431][biodb::testThat]
biodb.INFO [2023-04-11 18:54:12.432][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-11 18:54:12.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:12.434][biodb::testThat]
biodb.INFO [2023-04-11 18:54:12.441][biodb::testThat]
biodb.INFO [2023-04-11 18:54:12.442][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-11 18:54:12.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:12.444][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:12.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:12.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:12.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:12.452][private$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[2023-04-11 18:54:13.027][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[2023-04-11 18:54:13.788][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:13.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-04-11 18:54:13.808][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-04-11 18:54:13.825][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:13.827][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:13.828][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:13.829][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:13.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:13.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:13.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:13.833][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:13.834][biodb::testThat]
biodb.INFO [2023-04-11 18:54:13.835][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-11 18:54:13.836][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:13.837][biodb::testThat]
biodb.ERROR[2023-04-11 18:54:13.851][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-11 18:54:13.868][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-11 18:54:13.879][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:54:13.880][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-11 18:54:13.881][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-11 18:54:13.882][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:54:13.883][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:13.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:13.895][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:13.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:13.897][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:54:13.908][biodb::testContext]
biodb.INFO [2023-04-11 18:54:13.909][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:54:13.910][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-04-11 18:54:13.911][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:54:13.912][biodb::testContext]
biodb.INFO [2023-04-11 18:54:13.917][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:54:13.918][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:54:13.922][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:13.923][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:54:13.924][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:54:13.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.928][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:54:13.929][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:54:13.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.932][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[2023-04-11 18:54:13.933][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:54:13.934][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:54:13.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.937][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:54:13.938][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:54:13.939][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:54:13.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.943][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:54:13.944][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:54:13.945][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:54:13.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.948][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:54:13.949][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:54:13.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.953][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:54:13.954][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:54:13.955][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:54:13.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.959][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:54:13.960][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:54:13.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.962][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[2023-04-11 18:54:13.963][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:54:13.964][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:54:13.965][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:54:13.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.969][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:54:13.970][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:54:13.971][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:54:13.972][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:54:13.973][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:54:13.974][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:54:13.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.977][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:54:13.978][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:54:13.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.982][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:54:13.983][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:54:13.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.987][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:54:13.988][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:54:13.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.991][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:54:13.992][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:54:13.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:13.996][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:54:13.997][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:54:13.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:13.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:13.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.000][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:54:14.001][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:54:14.005][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:54:14.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.008][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:54:14.009][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:54:14.010][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:54:14.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.014][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:54:14.016][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.017][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:54:14.018][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:14.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.024][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:54:14.025][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:14.026][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.027][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:54:14.028][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:14.029][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.030][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.031][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:14.031][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:14.031][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:14.031][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:54:14.031][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:54:14.032][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:14.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:14.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.039][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:14.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:14.042][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.043][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.044][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:54:14.046][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.047][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:54:14.048][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.049][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:14.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.052][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.053][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:54:14.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:14.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.057][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:54:14.058][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:14.059][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.060][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.067][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:14.067][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:14.067][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:14.067][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:54:14.067][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:54:14.068][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:14.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:14.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.074][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.075][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:14.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:14.077][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.078][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.080][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:54:14.081][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.082][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:54:14.083][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:14.086][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.087][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.088][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.090][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:54:14.091][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:14.092][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.093][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:54:14.094][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:14.095][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.096][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.097][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.098][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:14.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:14.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.105][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:14.107][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:14.108][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.109][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.110][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:54:14.112][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.113][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:54:14.114][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:14.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.117][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.118][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.119][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.120][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:54:14.121][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:14.122][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.123][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:54:14.124][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:14.125][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.127][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.128][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:14.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.131][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:14.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.133][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.134][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.135][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:14.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:14.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.138][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:14.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:14.141][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.142][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[2023-04-11 18:54:14.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.169][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.DEBUG[2023-04-11 18:54:14.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.196][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.DEBUG[2023-04-11 18:54:14.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.210][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.DEBUG[2023-04-11 18:54:14.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.220][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:54:14.221][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:54:14.223][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:54:14.224][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:54:14.226][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:54:14.227][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:54:14.228][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:54:14.235][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:54:14.236][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:54:14.238][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:54:14.239][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:54:14.240][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:54:14.242][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:54:14.243][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:54:14.244][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:54:14.246][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:54:14.247][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:54:14.248][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:54:14.250][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:54:14.251][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:54:14.253][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:54:14.254][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:54:14.255][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:54:14.257][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:54:14.258][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:54:14.259][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:54:14.261][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:54:14.262][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:54:14.263][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:54:14.265][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:54:14.266][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:54:14.267][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:54:14.269][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:54:14.270][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:54:14.271][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:54:14.273][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:54:14.274][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:54:14.275][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:54:14.277][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:54:14.278][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:54:14.279][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:54:14.281][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:54:14.282][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:54:14.283][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:54:14.285][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:54:14.286][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:54:14.287][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:54:14.289][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:54:14.290][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:54:14.291][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:54:14.293][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:54:14.294][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:54:14.295][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:54:14.297][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:54:14.298][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:54:14.300][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:54:14.301][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:54:14.302][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:54:14.304][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:54:14.305][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:54:14.306][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:54:14.308][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:54:14.309][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:54:14.311][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:54:14.312][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:54:14.313][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:54:14.315][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:54:14.316][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:54:14.317][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:54:14.319][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:54:14.320][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:54:14.322][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:54:14.323][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:54:14.324][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:54:14.326][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:54:14.327][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:54:14.328][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:54:14.330][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:54:14.331][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:54:14.333][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:54:14.334][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:54:14.335][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:54:14.337][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:54:14.338][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:54:14.340][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:54:14.341][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:14.342][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.343][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.444][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[2023-04-11 18:54:14.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.471][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.DEBUG[2023-04-11 18:54:14.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.478][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[2023-04-11 18:54:14.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:14.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:14.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:14.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:14.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:14.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:14.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:14.486][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-11 18:54:14.497][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-11 18:54:14.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.501][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:14.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.507][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.508][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-11 18:54:14.509][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:54:14.510][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:14.511][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.512][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-11 18:54:14.513][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-11 18:54:14.514][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-11 18:54:14.515][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:14.516][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:14.516][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:14.516][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:14.518][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:54:14.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:14.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:14.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:14.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:14.525][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:54:14.525][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-11 18:54:14.526][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:14.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:14.528][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:14.529][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-11 18:54:14.529][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-11 18:54:14.530][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:54:14.532][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:54:14.534][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-11 18:54:14.535][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:54:14.537][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:54:14.539][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:54:14.543][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-11 18:54:14.544][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-11 18:54:14.545][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-11 18:54:14.547][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-11 18:54:14.548][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:54:14.549][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:54:14.551][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-11 18:54:14.552][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-11 18:54:14.553][biodb::testThat]
biodb.INFO [2023-04-11 18:54:14.554][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-04-11 18:54:14.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:14.556][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:14.561][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-11 18:54:14.565][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:14.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:14.568][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-04-11 18:54:15.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-04-11 18:54:15.792][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:15.807][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-04-11 18:54:15.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-04-11 18:54:15.833][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:15.837][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:15.838][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:15.840][private$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[2023-04-11 18:54:16.333][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[2023-04-11 18:54:16.835][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:16.843][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-04-11 18:54:16.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-04-11 18:54:16.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:16.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:16.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:16.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:16.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:16.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:16.868][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[2023-04-11 18:54:16.870][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[2023-04-11 18:54:16.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:16.874][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:16.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:54:17.367][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:54:17.914][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:17.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-04-11 18:54:17.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-04-11 18:54:17.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:17.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:17.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:17.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:17.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:17.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:17.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:17.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:17.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:17.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:17.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:18.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:18.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:18.001][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.DEBUG[2023-04-11 18:54:18.006][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:18.009][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:18.010][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-04-11 18:54:18.011][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:18.013][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-04-11 18:54:18.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:18.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:18.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:18.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:18.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:18.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:18.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:18.028][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:18.031][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:18.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-04-11 18:54:18.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:18.035][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-04-11 18:54:18.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:18.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:18.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:18.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:18.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:18.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:18.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:18.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:18.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:18.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:18.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:18.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:18.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:18.056][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[2023-04-11 18:54:18.059][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:18.062][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:18.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-04-11 18:54:18.065][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:18.066][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-04-11 18:54:18.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:18.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:18.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:18.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:18.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:18.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:18.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:18.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:18.082][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:18.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-04-11 18:54:18.085][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:18.086][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-04-11 18:54:18.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:18.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:18.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:18.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:18.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:18.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:18.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:18.100][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:18.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:18.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:18.112][private$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[2023-04-11 18:54:19.350][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[2023-04-11 18:54:19.917][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:19.927][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-04-11 18:54:19.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-04-11 18:54:19.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:19.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:19.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:19.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:19.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:19.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:19.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:54:19.980][biodb::testThat]
biodb.INFO [2023-04-11 18:54:19.982][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-04-11 18:54:19.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:19.985][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:19.990][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[2023-04-11 18:54:19.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:19.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:20.002][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:54:21.147][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:54:21.673][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:21.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-04-11 18:54:21.693][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-04-11 18:54:21.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:21.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:21.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:21.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:21.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:21.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:21.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:21.733][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:21.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:21.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:21.739][private$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[2023-04-11 18:54:22.237][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[2023-04-11 18:54:22.757][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:22.769][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-04-11 18:54:22.787][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-04-11 18:54:22.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:22.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:22.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:22.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:22.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:22.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:54:22.814][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:54:22.816][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-11 18:54:22.818][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-11 18:54:22.819][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:54:22.821][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:22.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:22.823][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:22.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:22.826][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:54:22.833][biodb::testContext]
biodb.INFO [2023-04-11 18:54:22.834][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:54:22.836][biodb::testContext] Test context - Test web services
biodb.INFO [2023-04-11 18:54:22.837][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:54:22.839][biodb::testContext]
biodb.INFO [2023-04-11 18:54:22.846][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:54:22.849][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:54:22.855][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:22.856][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:54:22.858][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:54:22.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.861][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:54:22.862][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:54:22.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.866][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:54:22.867][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:54:22.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.871][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:54:22.872][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:54:22.873][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:54:22.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.876][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:54:22.877][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:54:22.878][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:54:22.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.882][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:54:22.883][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:54:22.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.886][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:54:22.887][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:54:22.888][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:54:22.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.891][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:54:22.892][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:54:22.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.896][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:54:22.897][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:54:22.898][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:54:22.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.901][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:54:22.902][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:54:22.903][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:54:22.904][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:54:22.905][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:54:22.906][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:54:22.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.919][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:54:22.920][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:54:22.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.923][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:54:22.924][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:54:22.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.928][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:54:22.929][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:54:22.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.932][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:54:22.933][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:54:22.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.936][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[2023-04-11 18:54:22.937][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:54:22.938][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:54:22.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.941][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:54:22.942][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:54:22.945][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:54:22.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.948][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:54:22.949][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:54:22.950][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:54:22.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:22.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:22.954][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:54:22.956][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:22.957][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:54:22.957][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.958][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:22.959][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.960][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:22.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:22.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:22.963][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:54:22.964][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:22.965][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.966][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:54:22.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:22.968][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:22.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:22.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:22.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:22.970][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:54:22.970][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:54:22.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:22.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:22.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:22.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:22.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:22.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:22.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:22.977][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:22.978][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:22.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:22.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:22.980][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:22.981][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:54:22.983][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:22.984][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:54:22.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:22.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:22.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:22.990][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:22.991][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:54:22.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:22.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.993][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:54:22.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:22.995][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:22.996][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:22.997][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:22.997][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:22.997][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:22.997][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:54:22.997][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:54:22.998][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:22.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:23.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.004][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:23.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:23.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.008][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.009][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:54:23.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:54:23.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:23.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.018][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:54:23.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:23.020][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.021][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:54:23.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:23.023][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.024][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.025][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:23.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:23.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.032][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.033][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:23.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:23.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.036][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.037][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:54:23.039][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.040][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:54:23.041][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.042][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:23.043][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.045][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.046][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.047][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:54:23.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:23.049][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.050][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:54:23.051][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:23.052][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.053][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.054][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:23.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.057][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:23.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.060][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.061][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:23.063][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:23.064][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.065][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:23.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:23.068][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.120][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[2023-04-11 18:54:23.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.128][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[2023-04-11 18:54:23.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.133][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[2023-04-11 18:54:23.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.150][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:54:23.151][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:54:23.153][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:54:23.154][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:54:23.155][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:54:23.157][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:54:23.158][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:54:23.159][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:54:23.160][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:54:23.162][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:54:23.163][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:54:23.164][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:54:23.166][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:54:23.167][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:54:23.168][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:54:23.169][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:54:23.171][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:54:23.172][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:54:23.173][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:54:23.175][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:54:23.176][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:54:23.177][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:54:23.179][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:54:23.180][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:54:23.181][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:54:23.183][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:54:23.184][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:54:23.185][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:54:23.186][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:54:23.188][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:54:23.189][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:54:23.191][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:54:23.192][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:54:23.193][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:54:23.194][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:54:23.196][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:54:23.197][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:54:23.198][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:54:23.200][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:54:23.201][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:54:23.202][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:54:23.204][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:54:23.205][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:54:23.206][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:54:23.208][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:54:23.209][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:54:23.210][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:54:23.212][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:54:23.214][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:54:23.216][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:54:23.217][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:54:23.219][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:54:23.220][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:54:23.221][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:54:23.223][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:54:23.224][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:54:23.226][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:54:23.227][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:54:23.228][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:54:23.230][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:54:23.231][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:54:23.239][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:54:23.241][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:54:23.242][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:54:23.244][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:54:23.245][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:54:23.246][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:54:23.248][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:54:23.249][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:54:23.250][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:54:23.252][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:54:23.253][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:54:23.254][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:54:23.256][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:54:23.257][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:54:23.258][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:54:23.260][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:54:23.261][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:54:23.262][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:54:23.264][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:54:23.265][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:54:23.266][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:54:23.268][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:54:23.269][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:54:23.271][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:54:23.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:23.273][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.275][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.276][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.DEBUG[2023-04-11 18:54:23.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.294][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[2023-04-11 18:54:23.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.300][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[2023-04-11 18:54:23.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.306][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[2023-04-11 18:54:23.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.312][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[2023-04-11 18:54:23.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.318][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[2023-04-11 18:54:23.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.323][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[2023-04-11 18:54:23.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.329][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[2023-04-11 18:54:23.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.335][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[2023-04-11 18:54:23.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.341][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[2023-04-11 18:54:23.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.364][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.DEBUG[2023-04-11 18:54:23.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:23.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.376][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[2023-04-11 18:54:23.377][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-11 18:54:23.379][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-11 18:54:23.381][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.382][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.383][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:23.384][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.385][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.386][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.387][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-11 18:54:23.388][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:54:23.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:23.395][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.397][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-11 18:54:23.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-11 18:54:23.399][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-11 18:54:23.400][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:23.401][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:23.401][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:23.401][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:23.402][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:54:23.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.404][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:23.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:23.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:23.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:23.408][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:54:23.408][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-11 18:54:23.409][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:23.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:23.411][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:23.412][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-11 18:54:23.412][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-11 18:54:23.413][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:54:23.414][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:54:23.416][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-11 18:54:23.417][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:54:23.419][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:54:23.420][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:54:23.423][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-11 18:54:23.424][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-11 18:54:23.425][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-11 18:54:23.426][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-11 18:54:23.427][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:54:23.428][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:54:23.430][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-11 18:54:23.430][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-11 18:54:23.432][biodb::testThat]
biodb.INFO [2023-04-11 18:54:23.433][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-04-11 18:54:23.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:23.434][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:23.438][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-11 18:54:23.441][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:23.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-11 18:54:23.443][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:23.445][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-11 18:54:23.448][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[2023-04-11 18:54:23.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:23.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:23.453][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-11 18:54:23.947][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-11 18:54:24.448][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:24.455][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-04-11 18:54:24.465][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-04-11 18:54:24.472][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:54:24.474][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-11 18:54:24.475][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-11 18:54:24.476][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:54:24.477][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:24.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:24.478][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.480][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:54:24.485][biodb::testContext]
biodb.INFO [2023-04-11 18:54:24.486][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:54:24.487][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-04-11 18:54:24.488][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:54:24.488][biodb::testContext]
biodb.INFO [2023-04-11 18:54:24.493][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:54:24.495][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:54:24.499][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:24.501][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:54:24.502][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:54:24.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.507][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:54:24.509][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:54:24.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.514][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:54:24.516][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:54:24.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.532][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[2023-04-11 18:54:24.534][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:54:24.536][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:54:24.537][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:54:24.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.543][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:54:24.544][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:54:24.546][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:54:24.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.549][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[2023-04-11 18:54:24.550][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:54:24.551][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:54:24.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.557][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:54:24.558][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:54:24.559][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:54:24.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.565][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:54:24.566][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:54:24.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.572][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:54:24.573][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:54:24.575][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:54:24.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.579][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[2023-04-11 18:54:24.580][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:54:24.581][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:54:24.583][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:54:24.584][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:54:24.586][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:54:24.587][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:54:24.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.593][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:54:24.594][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:54:24.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.599][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:54:24.601][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:54:24.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.606][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:54:24.608][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:54:24.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.613][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:54:24.614][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:54:24.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.619][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:54:24.621][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:54:24.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.625][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:54:24.626][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:54:24.629][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:54:24.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.633][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:54:24.633][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:54:24.634][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:54:24.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.638][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:54:24.640][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.641][self$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[2023-04-11 18:54:24.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:24.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.647][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:54:24.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:24.649][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.650][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:54:24.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:24.652][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.652][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.653][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:24.653][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:24.653][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:24.653][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:54:24.653][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:54:24.654][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:24.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.657][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:24.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.660][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.661][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:24.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:24.663][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.664][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.665][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:54:24.667][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.668][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:54:24.669][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.670][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:24.671][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.674][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:54:24.675][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:24.676][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.677][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:54:24.678][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:24.679][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.680][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.681][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:24.681][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:24.681][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:24.681][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:54:24.681][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:54:24.682][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:24.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:24.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.689][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.690][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:24.691][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:24.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.696][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.698][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:54:24.701][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.702][self$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[2023-04-11 18:54:24.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.704][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:24.705][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.706][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.707][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.708][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.709][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:54:24.711][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:24.712][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.713][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:54:24.714][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:24.715][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.716][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.717][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.718][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:24.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:24.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.740][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.743][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:24.745][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:24.746][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.747][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.749][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:54:24.750][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.751][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:54:24.752][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.753][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:24.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.756][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.757][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.758][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.759][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:54:24.760][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:24.761][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.762][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:54:24.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:24.764][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:24.766][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.767][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:54:24.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.769][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:24.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:24.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:24.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:24.773][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.774][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:24.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:24.776][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:24.777][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:54:24.779][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:24.780][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.786][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[2023-04-11 18:54:24.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.795][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[2023-04-11 18:54:24.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.817][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[2023-04-11 18:54:24.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.822][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[2023-04-11 18:54:24.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.836][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[2023-04-11 18:54:24.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.840][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[2023-04-11 18:54:24.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.850][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[2023-04-11 18:54:24.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.860][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:54:24.862][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:54:24.863][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:54:24.865][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:54:24.866][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:54:24.868][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:54:24.869][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:54:24.871][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:54:24.872][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:54:24.874][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:54:24.876][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:54:24.877][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:54:24.878][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:54:24.880][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:54:24.881][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:54:24.883][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:54:24.884][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:54:24.885][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:54:24.887][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:54:24.888][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:54:24.890][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:54:24.891][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:54:24.892][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:54:24.894][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:54:24.895][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:54:24.897][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:54:24.898][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:54:24.899][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:54:24.901][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:54:24.909][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:54:24.911][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:54:24.913][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:54:24.914][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:54:24.916][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:54:24.917][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:54:24.918][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:54:24.920][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:54:24.921][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:54:24.922][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:54:24.923][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:54:24.925][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:54:24.926][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:54:24.928][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:54:24.929][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:54:24.930][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:54:24.932][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:54:24.933][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:54:24.935][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:54:24.936][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:54:24.937][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:54:24.939][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:54:24.940][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:54:24.941][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:54:24.943][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:54:24.944][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:54:24.945][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:54:24.947][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:54:24.948][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:54:24.949][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:54:24.951][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:54:24.952][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:54:24.953][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:54:24.955][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:54:24.956][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:54:24.957][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:54:24.958][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:54:24.960][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:54:24.961][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:54:24.962][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:54:24.964][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:54:24.965][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:54:24.966][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:54:24.968][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:54:24.969][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:54:24.970][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:54:24.972][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:54:24.973][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:54:24.974][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:54:24.976][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:54:24.977][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:54:24.978][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:54:24.980][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:54:24.981][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:54:24.983][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:54:24.984][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:54:24.985][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:54:24.986][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.988][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:24.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:24.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:24.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:24.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:24.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:24.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:24.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:24.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:24.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.001][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.DEBUG[2023-04-11 18:54:25.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.013][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[2023-04-11 18:54:25.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.044][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[2023-04-11 18:54:25.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.050][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[2023-04-11 18:54:25.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.056][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[2023-04-11 18:54:25.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.072][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.DEBUG[2023-04-11 18:54:25.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.079][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[2023-04-11 18:54:25.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.092][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[2023-04-11 18:54:25.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:54:25.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.104][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[2023-04-11 18:54:25.105][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-11 18:54:25.107][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-11 18:54:25.109][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:25.110][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:54:25.111][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:25.112][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:54:25.113][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:25.114][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:54:25.115][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:25.116][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-11 18:54:25.117][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:54:25.118][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:54:25.119][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:25.120][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-11 18:54:25.121][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-11 18:54:25.123][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:54:25.124][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:54:25.124][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:54:25.124][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:54:25.125][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:54:25.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:25.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:25.127][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:54:25.128][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:54:25.129][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:54:25.130][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:54:25.131][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:54:25.131][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-11 18:54:25.132][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:54:25.133][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:54:25.134][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:54:25.134][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-11 18:54:25.134][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-11 18:54:25.136][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:54:25.137][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:54:25.139][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-11 18:54:25.140][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:54:25.142][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:54:25.143][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:54:25.146][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-11 18:54:25.147][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-11 18:54:25.148][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-11 18:54:25.150][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-11 18:54:25.151][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:54:25.152][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:54:25.153][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-11 18:54:25.154][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-11 18:54:25.156][biodb::testThat]
biodb.INFO [2023-04-11 18:54:25.157][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-04-11 18:54:25.157][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:25.158][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:25.162][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-11 18:54:25.166][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:25.167][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-11 18:54:25.168][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:25.170][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-11 18:54:25.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-11 18:54:25.177][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:25.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-04-11 18:54:25.179][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:25.180][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-04-11 18:54:25.184][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-04-11 18:54:25.185][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:54:25.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-04-11 18:54:25.187][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:54:25.189][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:54:25.190][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:54:25.191][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-11 18:54:25.192][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:54:25.192][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:54:25.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:25.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:25.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:25.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:25.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:25.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:25.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:25.207][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-04-11 18:54:25.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:25.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:25.212][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-04-11 18:54:26.170][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-04-11 18:54:27.095][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:27.103][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-04-11 18:54:27.115][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-04-11 18:54:27.125][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-04-11 18:54:27.129][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:54:27.146][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:54:27.148][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-11 18:54:27.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:27.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:27.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:27.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:27.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:27.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:27.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:27.165][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.167][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.168][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.179][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:27.180][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:27.181][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.182][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-11 18:54:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-11 18:54:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.193][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:27.194][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:27.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.196][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:27.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:27.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.206][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:54:27.207][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:54:27.208][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.210][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:54:27.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:54:27.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.215][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.216][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:27.217][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:27.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.219][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.221][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:27.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.229][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:27.231][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:27.232][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.233][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.234][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-11 18:54:27.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:27.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.242][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:27.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:27.244][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.245][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:27.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:27.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.255][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:27.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:27.257][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.258][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:27.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:27.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.281][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:27.282][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:27.283][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.284][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.285][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-11 18:54:27.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-11 18:54:27.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.293][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:27.294][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:27.295][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.296][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:54:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:54:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:27.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:27.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:27.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:27.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:27.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:27.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:27.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:27.346][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-04-11 18:54:27.347][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:54:27.348][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-11 18:54:27.349][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-11 18:54:27.350][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:54:27.351][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:27.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:27.353][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:27.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:27.354][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:27.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
>
> proc.time()
user system elapsed
28.514 1.086 77.765
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.086 | 0.088 | 2.272 | |
| ChebiEntry | 0.213 | 0.000 | 0.214 | |