| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:14:53 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 179/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.5.0 (landing page) Pierrick Roger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | 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/library --timings biodbChebi_1.5.0.tar.gz |
| StartedAt: 2023-02-06 18:59:52 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 19:03:22 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 210.3 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/library --timings biodbChebi_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 2.841 0.206 5.223
* 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/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2023-02-06 19:00:51.998][biodb::testContext]
biodb.INFO [2023-02-06 19:00:52.001][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:00:52.003][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-02-06 19:00:52.005][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:00:52.006][biodb::testContext]
biodb.INFO [2023-02-06 19:00:52.027][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:00:52.030][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:00:52.040][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:00:52.042][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:00:52.043][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:00:52.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.049][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:00:52.078][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:00:52.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.082][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[2023-02-06 19:00:52.084][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:00:52.085][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:00:52.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.091][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:00:52.092][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:00:52.094][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:00:52.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.099][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:00:52.101][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:00:52.102][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:00:52.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.108][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:00:52.110][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:00:52.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.115][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:00:52.116][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:00:52.118][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:00:52.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.123][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:00:52.125][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:00:52.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.130][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:00:52.132][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:00:52.133][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:00:52.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.139][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:00:52.141][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:00:52.142][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:00:52.143][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:00:52.145][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:00:52.147][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:00:52.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.151][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[2023-02-06 19:00:52.152][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:00:52.154][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:00:52.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.159][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:00:52.161][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:00:52.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.165][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[2023-02-06 19:00:52.166][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:00:52.168][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:00:52.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.173][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:00:52.175][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:00:52.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.180][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:00:52.182][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:00:52.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.188][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:00:52.189][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:00:52.233][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:00:52.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.239][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:00:52.240][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:00:52.242][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:00:52.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.259][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:00:52.385][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.407][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-06 19:00:52.409][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:00:52.411][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.413][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.414][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.417][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:00:52.419][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:00:52.420][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.421][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:00:52.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:00:52.424][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:00:52.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:00:52.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:00:52.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:00:52.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:00:52.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:00:52.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.432][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:00:52.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.436][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.438][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:00:52.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:00:52.441][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.443][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.445][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:00:52.447][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.448][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:00:52.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:00:52.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.455][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.458][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:00:52.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:00:52.461][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.462][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:00:52.463][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:00:52.465][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.466][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.468][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:00:52.468][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:00:52.468][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:00:52.468][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:00:52.468][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:00:52.469][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:00:52.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:00:52.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.478][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.480][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:00:52.481][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:00:52.482][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.484][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.485][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:00:52.488][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.489][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-06 19:00:52.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:00:52.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.495][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.496][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.498][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.499][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:00:52.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:00:52.502][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.503][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:00:52.505][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:00:52.506][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.508][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.509][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.510][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:00:52.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.514][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:00:52.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.520][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:00:52.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:00:52.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.525][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.527][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:00:52.529][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.531][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:00:52.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:00:52.535][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.540][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:00:52.542][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:00:52.543][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.545][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:00:52.546][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:00:52.547][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.549][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:52.550][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.551][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:00:52.553][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.554][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.555][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:00:52.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:52.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:52.559][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:00:52.561][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.562][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:00:52.563][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:00:52.565][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:52.566][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:00:52.572][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:00:52.573][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.593][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[2023-02-06 19:00:52.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.605][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[2023-02-06 19:00:52.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.611][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[2023-02-06 19:00:52.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.617][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[2023-02-06 19:00:52.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.687][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:00:52.694][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:00:52.696][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:00:52.698][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:00:52.700][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:00:52.702][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:00:52.704][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:00:52.706][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:00:52.708][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:00:52.710][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:00:52.712][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:00:52.714][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:00:52.716][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:00:52.718][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:00:52.720][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:00:52.722][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:00:52.724][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:00:52.726][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:00:52.728][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:00:52.730][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:00:52.732][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:00:52.734][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:00:52.736][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:00:52.738][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:00:52.740][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:00:52.742][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:00:52.744][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:00:52.746][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:00:52.749][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:00:52.751][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:00:52.753][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:00:52.755][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:00:52.757][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:00:52.759][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:00:52.761][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:00:52.763][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:00:52.765][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:00:52.767][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:00:52.769][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:00:52.771][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:00:52.773][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:00:52.775][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:00:52.777][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:00:52.779][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:00:52.781][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:00:52.783][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:00:52.785][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:00:52.787][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:00:52.789][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:00:52.791][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:00:52.793][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:00:52.795][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:00:52.797][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:00:52.799][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:00:52.802][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:00:52.804][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:00:52.806][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:00:52.808][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:00:52.810][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:00:52.812][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:00:52.814][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:00:52.816][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:00:52.818][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:00:52.820][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:00:52.822][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:00:52.824][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:00:52.826][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:00:52.828][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:00:52.830][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:00:52.833][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:00:52.835][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:00:52.837][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:00:52.839][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:00:52.841][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:00:52.843][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:00:52.846][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:00:52.848][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:00:52.850][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:00:52.852][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:00:52.854][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:00:52.856][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:00:52.858][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:00:52.860][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:00:52.882][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:00:52.884][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:00:52.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:00:52.890][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.893][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.909][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[2023-02-06 19:00:52.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.918][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[2023-02-06 19:00:52.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.927][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[2023-02-06 19:00:52.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.936][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[2023-02-06 19:00:52.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:52.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:52.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:52.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:52.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:52.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:52.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:52.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.045][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[2023-02-06 19:00:53.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:00:53.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:00:53.065][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-06 19:00:53.078][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-06 19:00:53.081][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:53.083][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:00:53.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:53.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:00:53.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:53.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:00:53.090][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:53.091][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-06 19:00:53.093][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:00:53.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:00:53.096][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:53.097][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-06 19:00:53.098][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-06 19:00:53.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-06 19:00:53.102][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:00:53.103][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:00:53.103][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:00:53.103][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:00:53.105][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:00:53.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:53.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:53.109][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:00:53.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:00:53.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:00:53.113][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:00:53.114][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:00:53.114][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-06 19:00:53.116][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:00:53.117][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:00:53.118][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:00:53.120][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-06 19:00:53.120][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-06 19:00:53.129][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:00:53.131][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:00:53.134][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-06 19:00:53.136][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:00:53.138][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:00:53.141][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:00:53.174][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-06 19:00:53.176][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-06 19:00:53.182][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-06 19:00:53.188][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-06 19:00:53.194][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:00:53.196][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:00:53.198][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-06 19:00:53.200][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-06 19:00:53.223][biodb::testThat]
biodb.INFO [2023-02-06 19:00:53.224][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-02-06 19:00:53.226][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:53.227][biodb::testThat]
biodb.TRACE[2023-02-06 19:00:53.247][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-02-06 19:00:53.254][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:00:53.259][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:00:53.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:00:53.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:53.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:53.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:53.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:53.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:53.344][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.TRACE[2023-02-06 19:00:53.358][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.380][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.383][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.411][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:53.413][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:53.414][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.415][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.466][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:53.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:53.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.475][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:53.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:53.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.480][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:53.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:53.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.491][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:53.493][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:53.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.495][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.507][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.508][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.511][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.522][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:53.524][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:53.525][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.527][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.529][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:53.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:53.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.538][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:00:53.540][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:53.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.542][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.544][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:00:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.554][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:53.556][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:53.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.558][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:53.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:53.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.570][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:53.571][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:53.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.574][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:53.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:53.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.586][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:00:53.587][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:53.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.590][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.592][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:00:53.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:53.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.601][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:53.603][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:53.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.606][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:53.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:00:53.769][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-02-06 19:00:53.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:53.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:53.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:53.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:53.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:53.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:00:53.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:00:53.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:00:53.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:00:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:00:53.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:00:53.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:00:53.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:00:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:53.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:53.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:53.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:53.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:53.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.036][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.047][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.049][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.114][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.132][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.135][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:54.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:54.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:54.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:54.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:54.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:54.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.201][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:54.202][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:54.204][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.205][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:54.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:54.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.265][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.270][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.274][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.329][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.331][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.357][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.389][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.391][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.392][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.393][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.421][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.426][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.428][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.429][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.430][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.447][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.452][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.463][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.464][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.472][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.473][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.495][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.506][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.507][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.509][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.510][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.511][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.526][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:54.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:54.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.532][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:54.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:54.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:54.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:54.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.542][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:54.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:54.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.546][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.548][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:54.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:54.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.579][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.580][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.583][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.615][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.617][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.618][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.619][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.635][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.637][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.639][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.647][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.649][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.651][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.659][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.660][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.663][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.670][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.672][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.674][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.682][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.684][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.685][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.686][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.694][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.695][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:54.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.698][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.706][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.707][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:54.709][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.710][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.717][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:54.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.722][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.736][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.738][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:54.739][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.740][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.748][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:54.750][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:54.751][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.753][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.761][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:54.762][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:54.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.765][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:00:54.774][biodb::testThat]
biodb.INFO [2023-02-06 19:00:54.775][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-02-06 19:00:54.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:54.778][biodb::testThat]
biodb.DEBUG[2023-02-06 19:00:54.797][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-02-06 19:00:54.807][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:00:54.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-02-06 19:00:54.814][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:00:54.816][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-02-06 19:00:54.818][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:00:54.875][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:00:54.877][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:00:54.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:00:54.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:00:54.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:00:54.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:00:54.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:00:54.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:00:54.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:00:54.897][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.898][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.899][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.901][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:54.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:54.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.934][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.935][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.937][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.938][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:00:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:00:54.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.949][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.950][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.953][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:00:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:00:54.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.963][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.966][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.968][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:54.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:54.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.980][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.982][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:54.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:54.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:54.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.002][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:55.004][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:55.005][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.007][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.008][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:00:55.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.018][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:00:55.019][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:55.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.022][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.024][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:00:55.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:55.035][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:55.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.037][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:55.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:55.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.048][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:55.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:55.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.053][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:55.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:55.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.064][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:00:55.066][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:55.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.068][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.070][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:00:55.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:00:55.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.079][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:55.081][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:55.082][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.083][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.085][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:00:55.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:00:55.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:55.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:55.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:00:55.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:00:55.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:00:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:00:55.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:00:55.155][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-02-06 19:00:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-02-06 19:00:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-02-06 19:00:55.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-02-06 19:00:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-02-06 19:00:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-02-06 19:00:55.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-02-06 19:00:55.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:00:55.182][biodb::testThat]
biodb.INFO [2023-02-06 19:00:55.183][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-02-06 19:00:55.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:55.186][biodb::testThat]
biodb.TRACE[2023-02-06 19:00:55.189][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:55.191][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:55.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.194][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:00:55.195][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-02-06 19:00:55.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:55.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:00:55.310][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-02-06 19:00:55.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-06 19:00:55.399][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:00:55.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-02-06 19:00:55.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:00:55.425][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-02-06 19:00:55.458][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[2023-02-06 19:00:55.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:00:55.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:00:55.466][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:00:56.607][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:00:57.700][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:00:57.711][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-02-06 19:00:57.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-02-06 19:00:57.750][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-02-06 19:00:57.770][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:57.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:00:57.774][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:57.775][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:57.776][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:57.778][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:57.779][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:57.781][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:00:57.783][biodb::testThat]
biodb.INFO [2023-02-06 19:00:57.785][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-02-06 19:00:57.786][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:57.788][biodb::testThat]
biodb.TRACE[2023-02-06 19:00:57.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:57.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:57.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:57.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:57.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:57.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:57.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:57.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:57.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:00:57.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:00:57.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:57.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:00:57.946][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:00:57.951][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:00:57.953][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-06 19:00:57.955][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:00:57.957][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-02-06 19:00:57.980][biodb::testThat]
biodb.INFO [2023-02-06 19:00:57.982][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-02-06 19:00:57.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:57.985][biodb::testThat]
biodb.TRACE[2023-02-06 19:00:58.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:58.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:58.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:58.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:58.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.070][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.075][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:00:58.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:00:58.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.080][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:00:58.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:00:58.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:58.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:58.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:00:58.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:00:58.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:00:58.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:00:58.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.147][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.153][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:00:58.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:00:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:00:58.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:00:58.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:00:58.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:00:58.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:00:58.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:00:58.174][biodb::testThat]
biodb.INFO [2023-02-06 19:00:58.176][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-02-06 19:00:58.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:58.178][biodb::testThat]
biodb.INFO [2023-02-06 19:00:58.185][biodb::testThat]
biodb.INFO [2023-02-06 19:00:58.187][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-02-06 19:00:58.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:58.189][biodb::testThat]
biodb.INFO [2023-02-06 19:00:58.197][biodb::testThat]
biodb.INFO [2023-02-06 19:00:58.198][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-02-06 19:00:58.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:00:58.201][biodb::testThat]
biodb.DEBUG[2023-02-06 19:00:58.206][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-02-06 19:00:59.145][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-02-06 19:01:00.815][biodb::testThat]
biodb.INFO [2023-02-06 19:01:00.816][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-02-06 19:01:00.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:00.819][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:01.637][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[2023-02-06 19:01:02.480][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:02.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:02.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.484][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.485][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:02.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:02.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.489][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:02.491][biodb::testThat]
biodb.INFO [2023-02-06 19:01:02.493][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-02-06 19:01:02.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:02.495][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:02.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:02.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:02.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:02.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:02.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:02.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:02.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:02.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:02.654][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:01:02.656][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-06 19:01:02.658][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:02.660][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-06 19:01:02.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:02.823][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:01:02.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-06 19:01:02.827][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:02.829][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-02-06 19:01:02.854][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:02.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:02.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:02.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:02.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:02.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:02.963][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:02.985][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:02.987][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:03.009][private$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[2023-02-06 19:01:03.761][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[2023-02-06 19:01:04.534][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:04.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-02-06 19:01:04.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-02-06 19:01:04.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:04.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:04.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:04.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:04.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:04.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:04.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:04.596][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-02-06 19:01:04.662][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:04.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-02-06 19:01:04.666][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:04.668][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:04.669][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:04.670][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:04.672][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:04.673][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:04.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:04.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:04.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:04.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:04.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:04.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:04.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:04.693][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-02-06 19:01:04.697][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:04.698][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:04.700][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-02-06 19:01:05.468][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-02-06 19:01:06.208][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:06.218][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-02-06 19:01:06.249][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-02-06 19:01:06.265][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-02-06 19:01:06.272][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:06.296][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:06.298][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:06.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:06.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:06.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:06.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:06.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:06.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:06.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:06.321][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.323][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.347][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.360][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:06.362][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:06.376][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.377][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.379][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:06.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:06.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.388][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:06.390][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:06.391][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.393][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.404][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:06.406][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:06.407][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.408][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:06.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.419][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:06.421][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:06.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.423][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:06.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:06.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.434][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:06.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:06.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.438][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.440][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:06.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.443][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.444][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.446][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:06.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:06.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:06.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.459][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:06.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.470][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:06.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:06.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.474][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.485][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:06.487][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:06.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.490][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.491][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:06.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.509][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:06.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:06.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.513][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.515][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:06.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:06.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:06.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:06.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:06.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:06.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:06.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:06.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:06.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:06.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:06.582][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-02-06 19:01:06.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:06.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:06.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:06.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:06.612][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[2023-02-06 19:01:06.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:06.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:06.621][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:01:07.439][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:01:08.258][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:08.267][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-02-06 19:01:08.313][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-02-06 19:01:08.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:08.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:08.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:08.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:08.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:08.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:08.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:08.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:08.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:08.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:08.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:08.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:08.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:08.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:08.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:08.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:08.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:08.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:08.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:08.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:08.381][private$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[2023-02-06 19:01:09.188][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[2023-02-06 19:01:09.969][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:09.979][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-02-06 19:01:09.995][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-02-06 19:01:10.070][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[2023-02-06 19:01:10.075][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:01:10.077][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-06 19:01:10.079][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:10.081][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-06 19:01:10.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:10.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:10.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:10.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:10.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:10.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:10.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:10.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:10.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:10.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:10.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:10.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:10.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:10.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:10.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:10.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:10.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:10.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:10.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:10.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:10.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:10.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:10.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:10.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:10.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:10.151][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[2023-02-06 19:01:10.153][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-02-06 19:01:10.154][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:10.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-02-06 19:01:10.158][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:10.160][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:10.161][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:10.163][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:10.164][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:10.165][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:10.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:10.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:10.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:10.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:10.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:10.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:10.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:10.231][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-02-06 19:01:10.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:10.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:10.239][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-02-06 19:01:11.057][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-02-06 19:01:11.857][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:11.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-02-06 19:01:11.882][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-02-06 19:01:11.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-02-06 19:01:11.902][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:11.924][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:11.925][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:11.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:11.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:11.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:11.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:11.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:11.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:11.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:11.945][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:11.947][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:11.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.949][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:11.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:11.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.961][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:11.963][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:11.964][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.965][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.967][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:11.969][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:11.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.971][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.973][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:11.975][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:11.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.977][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.979][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:11.981][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:11.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.983][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.985][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:11.986][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:11.988][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.989][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.991][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:11.992][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:11.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:11.995][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:11.997][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:11.998][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:12.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.001][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.003][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:12.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:12.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.007][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:12.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:12.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.018][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:12.020][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:12.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.023][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.034][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:12.035][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:12.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.049][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:12.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:12.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:12.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:12.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:12.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:12.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:12.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:12.117][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-02-06 19:01:12.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:12.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:12.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:12.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:12.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:12.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.210][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-02-06 19:01:12.211][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:12.213][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-02-06 19:01:12.215][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:12.217][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:12.218][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:12.220][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:12.221][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:12.222][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:12.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:12.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.243][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-02-06 19:01:12.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:12.248][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:12.250][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-02-06 19:01:13.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-02-06 19:01:13.926][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:13.950][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-02-06 19:01:13.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-02-06 19:01:13.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-02-06 19:01:13.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:14.023][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:14.030][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:14.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:14.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:14.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:14.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:14.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:14.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:14.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:14.049][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.051][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.053][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.064][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:14.066][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:14.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.069][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.070][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:14.072][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:14.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.075][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.077][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:14.078][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:14.080][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.081][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.083][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.084][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.086][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.087][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.089][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.090][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.093][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.095][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:14.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.098][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.099][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.105][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.107][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.108][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.109][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.111][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.122][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:14.124][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:14.125][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.126][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.128][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:14.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:14.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.139][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.142][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:14.211][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-02-06 19:01:14.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:14.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:14.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:14.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:14.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:14.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:14.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:14.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:14.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:14.259][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-02-06 19:01:14.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:14.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-02-06 19:01:14.264][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:14.266][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:14.267][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:14.269][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:14.270][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:14.272][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:14.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:14.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:14.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:14.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:14.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:14.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:14.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:14.292][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-02-06 19:01:14.295][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:14.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:14.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-02-06 19:01:15.253][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-02-06 19:01:16.070][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:16.117][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-02-06 19:01:16.132][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-02-06 19:01:16.145][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-02-06 19:01:16.151][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:16.172][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:16.174][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:16.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:16.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:16.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:16.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:16.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:16.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:16.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:16.194][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.195][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.198][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.209][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:16.211][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:16.212][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.213][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.215][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:16.217][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:16.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.219][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:16.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:16.224][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.225][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.229][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.231][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.233][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:16.235][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:16.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.237][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.239][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:16.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.243][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:16.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:16.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.249][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.251][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.254][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.255][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.267][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:16.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:16.270][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.271][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.273][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:16.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:16.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.282][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:16.283][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:16.285][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.286][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:16.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:16.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:16.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:16.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:16.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.360][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-02-06 19:01:16.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:16.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:16.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:16.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:16.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:16.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:16.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:16.406][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-02-06 19:01:16.408][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:16.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-02-06 19:01:16.412][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:16.413][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:16.415][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:16.416][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:16.418][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:16.419][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:16.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:16.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:16.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:16.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:16.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:16.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:16.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:16.440][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-02-06 19:01:16.444][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:16.445][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:16.448][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-02-06 19:01:17.204][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-02-06 19:01:17.945][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:17.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-02-06 19:01:17.968][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-02-06 19:01:17.997][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-02-06 19:01:18.002][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:18.025][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:18.027][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:18.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:18.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:18.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:18.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:18.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:18.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:18.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:18.047][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.051][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.062][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:18.063][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:18.064][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.066][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.068][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:18.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:18.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.077][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:18.079][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:18.080][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.081][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:18.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:18.094][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:18.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.097][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:18.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:18.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.108][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:18.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:18.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.112][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:18.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:18.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.124][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:18.125][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:18.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.128][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.130][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:18.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:18.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.139][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:18.141][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.143][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.145][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.155][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:18.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:18.158][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.159][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:18.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:18.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.170][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:18.172][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:18.173][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.175][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:18.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:18.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.187][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:18.188][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:18.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.191][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:18.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.210][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:18.212][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:18.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.215][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.217][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:18.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:18.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:18.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:18.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:18.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:18.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:18.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:18.288][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-02-06 19:01:18.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:18.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:18.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:18.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:18.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:18.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:18.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:18.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:18.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:18.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:18.324][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-02-06 19:01:18.325][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:18.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-02-06 19:01:18.330][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:18.331][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:18.333][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:18.334][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:18.336][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:18.337][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:18.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:18.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:18.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:18.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:18.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:18.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:18.357][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[2023-02-06 19:01:18.358][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-02-06 19:01:18.363][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:18.364][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:18.366][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-02-06 19:01:19.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-02-06 19:01:20.481][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:20.496][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-02-06 19:01:20.511][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-02-06 19:01:20.526][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-02-06 19:01:20.531][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:20.554][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:20.555][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:20.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:20.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:20.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:20.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:20.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:20.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:20.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:20.575][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.577][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.579][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.590][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:20.592][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:20.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.594][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.596][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:20.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:20.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.606][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:20.607][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:20.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.610][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.612][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:20.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:20.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.621][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:20.623][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:20.624][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.625][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:20.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:20.639][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.641][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:20.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:20.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.652][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:20.653][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:20.655][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.656][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.658][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:20.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:20.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.667][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:20.669][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.671][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.673][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:20.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.682][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:20.684][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:20.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.696][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:20.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:20.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.707][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:20.709][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:20.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.712][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:20.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:20.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.723][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:20.725][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:20.726][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.727][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.729][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:20.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:20.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.738][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:20.740][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:20.741][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.742][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.744][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:20.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:20.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:20.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:20.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:20.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:20.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:20.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:20.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:20.813][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-02-06 19:01:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:20.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:20.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:20.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:20.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:20.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:20.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:20.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:20.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:20.847][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-02-06 19:01:20.849][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:20.851][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-02-06 19:01:20.853][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:20.854][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:20.856][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:20.857][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:20.859][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:20.860][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:20.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:20.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:20.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:20.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:20.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:20.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:20.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:20.880][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-02-06 19:01:20.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:20.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:20.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-02-06 19:01:21.647][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-02-06 19:01:22.405][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:22.415][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-02-06 19:01:22.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-02-06 19:01:22.444][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-02-06 19:01:22.450][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:22.472][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:22.474][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:22.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:22.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:22.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:22.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:22.493][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.496][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.497][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.508][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:22.509][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:22.511][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.512][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.514][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:22.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:22.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.523][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:22.525][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:22.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.528][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:22.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:22.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.539][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:22.540][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:22.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.543][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:22.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:22.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:22.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:22.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.558][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:22.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:22.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.584][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:22.585][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:22.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.588][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.589][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:22.591][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.593][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.595][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:22.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.604][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:22.606][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:22.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.609][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.620][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:22.621][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:22.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.624][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:22.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.635][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:22.637][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:22.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.639][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.641][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:22.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:22.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.650][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:22.651][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:22.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.654][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.656][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:22.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:22.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:22.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:22.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:22.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:22.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:22.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:22.725][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-02-06 19:01:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:22.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:22.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:22.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:22.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:22.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.759][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-02-06 19:01:22.760][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:22.762][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-02-06 19:01:22.764][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:22.765][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:22.767][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:22.768][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:22.769][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:22.770][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:22.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:22.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:22.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:22.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.799][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-02-06 19:01:22.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:22.805][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:22.806][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-02-06 19:01:23.577][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-02-06 19:01:24.344][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:24.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-02-06 19:01:24.370][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-02-06 19:01:24.385][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-02-06 19:01:24.391][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:24.414][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:24.416][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:24.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:24.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:24.437][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.441][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.453][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:24.454][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:24.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.457][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.459][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:24.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:24.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.469][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:24.471][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:24.472][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.473][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:24.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:24.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.500][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:24.502][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:24.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.504][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:24.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:24.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.516][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:24.518][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:24.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.521][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:24.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:24.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.532][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:24.534][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:24.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.537][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.539][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:24.541][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.543][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.545][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:24.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.555][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:24.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:24.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.560][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:24.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:24.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.572][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.573][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.575][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.576][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.588][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:24.590][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:24.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.593][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.595][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:24.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:24.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.605][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:24.606][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:24.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.609][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:24.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:24.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:24.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:24.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:24.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:24.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:24.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:24.684][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-02-06 19:01:24.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:24.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:24.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:24.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.728][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-02-06 19:01:24.730][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:24.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-02-06 19:01:24.734][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:24.735][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:24.737][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:24.738][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:24.740][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:24.741][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:24.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:24.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.763][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-02-06 19:01:24.767][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:24.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:24.770][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-02-06 19:01:25.566][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-02-06 19:01:26.312][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:26.323][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-02-06 19:01:26.338][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-02-06 19:01:26.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-02-06 19:01:26.361][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:26.384][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:26.386][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:26.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:26.407][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.417][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.427][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.439][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:26.441][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:26.442][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.444][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.445][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:26.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:26.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.455][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.457][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.460][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.472][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.475][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.477][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.488][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.490][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.493][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.505][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.507][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.508][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.510][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.512][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:26.513][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.516][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:26.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.528][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.530][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.531][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.533][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.545][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.546][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.549][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.561][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:26.563][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:26.564][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.566][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:26.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:26.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.578][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.579][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.582][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.584][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.668][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-02-06 19:01:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:26.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:26.703][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-02-06 19:01:26.704][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:26.707][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-02-06 19:01:26.708][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:26.710][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:26.712][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:26.713][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:26.715][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:26.716][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:26.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:26.737][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-02-06 19:01:26.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:26.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:26.744][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-02-06 19:01:27.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-02-06 19:01:28.358][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:28.367][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-02-06 19:01:28.381][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-02-06 19:01:28.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-02-06 19:01:28.400][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:28.437][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:28.439][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:28.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:28.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:28.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:28.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:28.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:28.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:28.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:28.458][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.460][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.462][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.473][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:28.474][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:28.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.477][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.479][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:28.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:28.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.488][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:28.489][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:28.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.492][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:28.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:28.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:28.504][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:28.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.506][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:28.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:28.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.517][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:28.518][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:28.520][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.521][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:28.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:28.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.532][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:28.533][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:28.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.536][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.537][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:28.539][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.540][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.541][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.543][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:28.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.552][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:28.554][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:28.555][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.556][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:28.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:28.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.567][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:28.569][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:28.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.571][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:28.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.583][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:28.584][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:28.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.587][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:28.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:28.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.598][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:28.599][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:28.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.602][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.604][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:28.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:28.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:28.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:28.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:28.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:28.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:28.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:28.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:28.680][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-02-06 19:01:28.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:28.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:28.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:28.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:28.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:28.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:28.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:28.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:28.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:28.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:28.712][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-02-06 19:01:28.713][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:28.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-02-06 19:01:28.717][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:28.718][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:28.720][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:28.721][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:28.723][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:28.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:28.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:28.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:28.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:28.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:28.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:28.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:28.741][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[2023-02-06 19:01:28.743][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-02-06 19:01:28.747][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:28.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:28.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-02-06 19:01:29.568][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-02-06 19:01:30.355][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:30.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-02-06 19:01:30.394][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-02-06 19:01:30.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-02-06 19:01:30.415][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:30.452][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:30.454][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:30.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:30.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:30.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:30.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:30.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:30.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:30.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:30.490][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.492][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.495][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.506][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:30.508][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:30.509][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.511][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.513][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:30.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:30.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.522][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:30.523][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:30.525][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.526][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:30.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:30.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.537][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:30.539][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:30.540][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.542][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:30.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:30.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.553][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:30.554][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:30.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.557][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:30.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:30.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.569][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:30.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:30.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.573][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.575][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:30.576][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.579][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.581][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:30.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.591][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:30.592][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:30.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.595][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.606][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:30.608][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:30.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.611][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:30.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:30.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.623][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:30.625][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:30.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.627][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.629][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:30.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.649][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:30.651][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:30.652][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.653][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:30.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:30.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:30.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:30.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:30.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:30.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:30.760][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-02-06 19:01:30.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:30.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:30.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:30.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:30.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:30.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:30.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:30.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:30.834][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-02-06 19:01:30.835][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:30.837][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.INFO [2023-02-06 19:01:30.839][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-02-06 19:01:30.841][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:30.842][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:30.844][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:30.845][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:30.853][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:30.855][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:30.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:30.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:30.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:30.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:30.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:30.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:30.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:30.895][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-02-06 19:01:30.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:30.900][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:30.902][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-02-06 19:01:31.633][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-02-06 19:01:32.440][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:32.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-02-06 19:01:32.465][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-02-06 19:01:32.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-02-06 19:01:32.485][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:32.507][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:32.509][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:32.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:32.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:32.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:32.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:32.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:32.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:32.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:32.529][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.531][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.533][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.545][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:32.547][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:32.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.550][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:32.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:32.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.561][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:32.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:32.565][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.566][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:32.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:32.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:32.579][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:32.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.582][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:32.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:32.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.589][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.590][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:32.592][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:32.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.594][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.596][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:32.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.601][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.602][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:32.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:32.613][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:32.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.616][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:32.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:32.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.627][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:32.640][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:32.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.643][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:32.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.656][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:32.658][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:32.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.661][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.662][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:32.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:32.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.672][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:32.673][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:32.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.676][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:32.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:32.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:32.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:32.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:32.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:32.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:32.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:32.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:32.739][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-02-06 19:01:32.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:32.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:32.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:32.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:32.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:32.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:32.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:32.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:32.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:32.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:32.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:32.773][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-02-06 19:01:32.775][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:32.777][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-02-06 19:01:32.779][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:32.780][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:32.782][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:32.783][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:32.785][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:32.786][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:32.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:32.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:32.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:32.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:32.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:32.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:32.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:32.806][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-02-06 19:01:32.810][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:32.811][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:32.813][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-02-06 19:01:33.576][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-02-06 19:01:34.354][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:34.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-02-06 19:01:34.379][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-02-06 19:01:34.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-02-06 19:01:34.398][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:34.421][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:34.422][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:34.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:34.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:34.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:34.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:34.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:34.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:34.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:34.442][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.444][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.447][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.458][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:34.459][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:34.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.462][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.464][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:34.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:34.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.474][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:34.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:34.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.478][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:34.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.489][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:34.490][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:34.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.493][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.495][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:34.497][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:34.498][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.499][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:34.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:34.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.505][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.507][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:34.509][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.511][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.513][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:34.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.523][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:34.524][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:34.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.538][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:34.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:34.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.550][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:34.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:34.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.554][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:34.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:34.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.566][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:34.568][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:34.569][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.570][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.572][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:34.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:34.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.582][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:34.583][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:34.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.586][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:34.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:34.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:34.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:34.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:34.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:34.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:34.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:34.680][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-02-06 19:01:34.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:34.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:34.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:34.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:34.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:34.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:34.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:34.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:34.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:34.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:34.714][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-02-06 19:01:34.715][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:34.717][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-02-06 19:01:34.719][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:34.721][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:34.722][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:34.724][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:34.725][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:34.726][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:34.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:34.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:34.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:34.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:34.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:34.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:34.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:34.746][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-02-06 19:01:34.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:34.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:34.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-02-06 19:01:35.739][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-02-06 19:01:36.550][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:36.560][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-02-06 19:01:36.590][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-02-06 19:01:36.604][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-02-06 19:01:36.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:36.631][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:36.633][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:36.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:36.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:36.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:36.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:36.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:36.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:36.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:36.652][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.654][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.655][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.656][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.667][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:36.668][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:36.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.671][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:36.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:36.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.682][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:36.683][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:36.685][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.686][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:36.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:36.700][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.701][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:36.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:36.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.712][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:36.714][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:36.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.716][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:36.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.727][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:36.728][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:36.730][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.731][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.733][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:36.734][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.736][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.738][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:36.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.747][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:36.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:36.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.751][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:36.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:36.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.762][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:36.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:36.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.767][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:36.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:36.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:36.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:36.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.783][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.785][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:36.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:36.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.795][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:36.797][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:36.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.800][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:36.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:36.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:36.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:36.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:36.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:36.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:36.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:36.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:36.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:36.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:36.876][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-02-06 19:01:36.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:36.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:36.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:36.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:36.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:36.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:36.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:36.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:36.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:36.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:36.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:36.912][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-02-06 19:01:36.913][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:36.916][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-02-06 19:01:36.918][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:36.919][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:36.921][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:36.922][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:36.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:36.925][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:36.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:36.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:36.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:36.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:36.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:36.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:36.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:36.946][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-02-06 19:01:36.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:36.952][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:36.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-02-06 19:01:37.754][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-02-06 19:01:38.628][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-02-06 19:01:38.635][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-02-06 19:01:38.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-02-06 19:01:38.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-02-06 19:01:38.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-02-06 19:01:38.672][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:38.694][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:38.695][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:38.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:38.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:38.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:38.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:38.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:38.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:38.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:38.715][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.719][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.730][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:38.731][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:38.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.734][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:38.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:38.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.745][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:38.746][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:38.748][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.749][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.751][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:38.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:38.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:38.762][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:38.763][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.764][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:38.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:38.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.775][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:38.777][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:38.778][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.779][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:38.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:38.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.795][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:38.796][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:38.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.799][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.801][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:38.802][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.804][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.805][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:38.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.816][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:38.817][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:38.818][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.820][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:38.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:38.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.831][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:38.832][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:38.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.835][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:38.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:38.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.846][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:38.848][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:38.849][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.851][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:38.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:38.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.862][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:38.864][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:38.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.867][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.869][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:38.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:38.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:38.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:38.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:38.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:38.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:38.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:38.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:38.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:38.936][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-02-06 19:01:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:38.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:38.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:38.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:38.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:38.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:38.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:38.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:38.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:38.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:38.977][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.DEBUG[2023-02-06 19:01:38.979][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-02-06 19:01:38.980][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:38.982][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-02-06 19:01:38.984][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:38.985][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:38.987][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:38.988][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:38.990][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:38.991][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:38.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:38.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:38.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:39.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:39.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:39.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:39.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:39.011][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-02-06 19:01:39.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:39.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:39.018][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-02-06 19:01:39.845][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-02-06 19:01:40.691][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:40.701][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-02-06 19:01:40.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-02-06 19:01:40.730][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-02-06 19:01:40.735][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:40.757][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:40.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:40.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:40.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:40.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:40.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:40.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:40.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:40.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:40.778][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.780][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.783][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.794][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:40.795][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:40.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.798][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.800][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:40.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:40.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.809][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:40.811][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:40.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.814][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:40.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:40.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:40.827][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:40.828][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.830][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:40.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.840][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:40.842][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:40.843][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.845][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:40.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:40.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.856][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:40.857][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:40.858][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.860][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.861][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:40.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:40.864][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.866][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.868][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:40.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:40.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.877][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:40.879][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:40.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.881][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:40.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:40.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.893][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:40.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:40.896][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.897][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:40.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:40.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.909][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:40.910][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:40.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.913][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.914][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:40.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:40.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.924][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:40.925][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:40.927][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.928][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.930][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:40.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:40.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:40.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:40.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:40.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:40.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:40.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:40.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:40.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:40.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:40.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:41.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:41.001][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-02-06 19:01:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:41.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:41.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:41.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:41.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:41.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:41.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:41.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:41.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:41.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:41.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:41.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:41.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:41.035][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-02-06 19:01:41.036][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:41.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-02-06 19:01:41.040][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:41.042][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:41.043][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:41.045][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:41.046][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:41.048][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:41.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:41.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:41.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:41.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:41.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:41.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:41.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:41.068][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-02-06 19:01:41.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:41.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:41.075][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-02-06 19:01:42.822][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-02-06 19:01:43.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:43.671][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-02-06 19:01:43.686][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-02-06 19:01:43.700][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-02-06 19:01:43.706][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:43.729][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:43.730][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:43.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:43.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:43.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:43.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:43.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:43.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:43.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:43.750][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.753][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.755][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.766][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:43.768][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:43.769][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.771][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.773][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:43.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.783][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:43.784][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:43.786][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.787][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:43.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:43.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.800][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:43.801][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:43.803][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.804][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:43.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:43.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.814][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:43.816][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:43.817][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.819][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:43.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:43.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.830][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:43.831][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:43.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.834][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.836][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:43.837][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.839][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.840][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:43.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:43.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:43.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.856][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:43.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:43.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.867][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:43.868][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:43.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.871][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:43.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:43.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.883][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:43.884][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:43.886][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.887][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:43.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:43.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:43.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.903][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:43.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:43.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:43.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:43.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:43.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:43.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:43.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:43.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:43.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:43.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:43.973][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-02-06 19:01:43.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:43.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:43.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:43.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:43.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:43.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:43.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:44.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:44.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:44.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:44.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:44.006][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-02-06 19:01:44.008][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:44.010][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-02-06 19:01:44.012][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:44.013][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:44.014][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:44.016][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:44.017][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:44.019][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:44.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:44.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:44.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:44.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:44.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:44.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:44.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:44.038][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-02-06 19:01:44.042][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:44.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:44.045][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-02-06 19:01:44.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-02-06 19:01:45.687][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:45.696][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-02-06 19:01:45.711][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-02-06 19:01:45.725][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-02-06 19:01:45.730][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:45.752][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:45.753][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:45.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:45.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:45.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:45.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:45.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:45.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:45.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:45.775][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.778][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.779][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.790][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:45.791][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:45.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.794][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.796][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:45.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:45.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.805][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:45.807][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:45.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.810][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:45.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:45.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.820][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:45.822][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:45.823][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.824][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:45.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:45.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.839][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:45.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:45.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.850][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:45.852][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:45.853][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.855][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.856][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:45.858][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:45.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.860][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.862][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:45.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:45.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.871][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:45.873][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:45.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.876][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:45.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:45.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.887][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:45.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:45.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.891][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:45.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.902][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:45.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:45.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.906][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:45.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:45.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.917][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:45.919][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:45.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.922][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:45.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:45.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:45.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:45.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:45.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:45.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:45.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:45.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:45.994][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-02-06 19:01:45.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:45.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:45.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:46.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:46.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:46.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:46.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:46.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:46.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:46.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:46.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:46.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:46.062][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[2023-02-06 19:01:46.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:46.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:46.071][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:01:47.106][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:01:48.024][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:48.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-02-06 19:01:48.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-02-06 19:01:48.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:48.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:48.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:48.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:48.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:48.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:48.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:48.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:48.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:48.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:48.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:48.843][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:48.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:48.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:48.852][private$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[2023-02-06 19:01:49.640][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[2023-02-06 19:01:50.417][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:50.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-02-06 19:01:50.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-02-06 19:01:50.451][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[2023-02-06 19:01:50.456][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:50.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:50.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:01:51.270][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:01:52.016][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:52.026][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-02-06 19:01:52.041][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-02-06 19:01:52.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:52.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:52.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:52.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:52.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:52.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:52.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:52.064][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-02-06 19:01:52.065][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:52.068][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-02-06 19:01:52.069][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:52.071][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:52.072][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:52.074][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:52.075][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:52.077][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:52.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:52.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:52.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:52.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:52.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:52.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:52.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:52.097][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-02-06 19:01:52.101][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:52.102][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:52.104][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-02-06 19:01:52.882][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-02-06 19:01:54.655][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:54.665][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-02-06 19:01:54.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-02-06 19:01:54.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-02-06 19:01:54.697][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:54.726][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:54.727][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:54.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:54.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:54.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:54.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:54.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:54.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:54.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:54.747][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.748][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.751][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.762][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:54.763][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:54.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.766][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:54.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.777][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:54.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:54.779][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.781][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:54.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.791][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:54.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:54.794][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.795][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:54.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:54.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.806][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:54.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:54.809][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.832][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:54.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:54.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.843][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:54.845][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:54.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.848][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.849][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.858][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:54.860][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:54.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.863][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.864][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:54.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.873][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:54.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:54.876][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.878][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:54.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:54.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.889][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:54.890][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:54.891][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.893][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:54.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:54.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.904][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:54.905][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:54.907][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.908][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.910][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:54.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:54.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.919][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:54.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:54.922][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.923][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:54.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:54.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:54.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:54.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:54.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:54.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:54.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:54.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:54.992][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-02-06 19:01:54.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:54.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:54.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:55.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:55.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:55.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:55.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:55.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:55.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:55.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:55.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:55.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:55.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:55.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:55.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:55.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:55.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:55.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:55.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:55.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:55.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:55.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:55.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:55.057][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-02-06 19:01:55.059][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:55.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-02-06 19:01:55.062][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:55.064][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:55.065][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:55.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:01:55.068][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:01:55.070][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:01:55.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:55.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:55.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:55.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:55.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:55.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:55.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:55.089][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-02-06 19:01:55.093][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:55.094][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:55.096][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-02-06 19:01:55.866][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-02-06 19:01:56.708][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:01:56.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-02-06 19:01:56.731][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-02-06 19:01:56.745][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-02-06 19:01:56.750][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:01:56.772][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:56.774][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:01:56.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:56.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:56.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:56.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:56.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:56.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.790][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.TRACE[2023-02-06 19:01:56.793][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:56.795][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:56.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.797][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:56.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:56.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.808][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:56.810][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:56.811][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.813][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.815][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:01:56.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:01:56.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.839][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:56.840][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:56.842][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.843][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.845][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:56.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:56.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.854][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:56.855][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:56.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.858][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:56.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:56.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.869][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:56.870][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:56.872][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.873][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:56.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:56.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.884][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:56.885][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:56.887][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.888][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.890][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:56.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:56.893][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.894][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.896][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:01:56.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:56.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.905][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:56.907][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:56.908][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.909][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:56.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:56.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.920][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:56.922][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:56.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.925][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:56.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.936][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:56.937][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:56.939][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.940][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:01:56.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:01:56.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.950][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:56.952][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:56.953][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.954][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.956][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:56.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:56.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:56.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:56.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:56.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:56.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:56.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:56.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:56.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:56.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:56.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:56.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:56.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:56.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:56.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:56.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:57.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:57.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:57.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:57.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.023][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-02-06 19:01:57.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.093][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:57.098][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:01:57.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-06 19:01:57.101][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:57.103][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-06 19:01:57.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.796][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:57.800][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:01:57.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-06 19:01:57.804][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:57.805][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-06 19:01:57.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:57.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:57.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.461][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:01:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:01:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:58.482][biodb::testThat]
biodb.INFO [2023-02-06 19:01:58.484][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-02-06 19:01:58.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:58.486][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:58.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:01:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:58.606][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:01:58.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:58.612][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:58.614][private$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[2023-02-06 19:01:59.404][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[2023-02-06 19:02:00.171][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:00.181][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-02-06 19:02:00.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-02-06 19:02:00.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:00.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:00.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:00.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:00.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:00.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:00.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:00.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:00.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:00.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:00.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:00.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:00.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:00.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:00.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:00.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:00.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:00.236][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[2023-02-06 19:02:00.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:00.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:00.245][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:02:01.017][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:02:02.423][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:02.433][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-02-06 19:02:02.449][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-02-06 19:02:02.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:02.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:02.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:02.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:02.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:02.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:02.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:02.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:02.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:02.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:02.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:02.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:02.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:02.514][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:02.518][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:02.520][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:02.523][private$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[2023-02-06 19:02:03.324][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[2023-02-06 19:02:04.083][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:04.093][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-02-06 19:02:04.109][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-02-06 19:02:04.116][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:04.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:04.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:04.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:04.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:04.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:04.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:04.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:04.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.173][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.175][private$selectFields]
biodb.TRACE[2023-02-06 19:02:04.176][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:04.177][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:04.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.181][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.182][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.184][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.186][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.188][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.189][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.191][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.193][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.194][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.197][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.198][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:04.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.230][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-02-06 19:02:04.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:04.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:04.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:04.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:04.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:04.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:04.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:04.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.259][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.260][private$selectFields]
biodb.TRACE[2023-02-06 19:02:04.261][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:04.263][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:04.264][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.267][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.270][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.275][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.277][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.278][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:04.279][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.282][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.284][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.285][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:04.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:04.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.304][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-06 19:02:04.305][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:04.307][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:04.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:04.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:04.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:04.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:04.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:04.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:04.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:04.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:04.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:04.510][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:04.512][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:04.514][private$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[2023-02-06 19:02:05.266][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[2023-02-06 19:02:06.024][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:06.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-02-06 19:02:06.065][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-02-06 19:02:06.074][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[2023-02-06 19:02:06.079][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:06.080][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:06.083][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:02:07.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:02:08.647][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:08.657][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-02-06 19:02:08.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-02-06 19:02:08.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:08.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:08.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:08.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:08.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:08.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:08.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:08.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:08.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:08.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:08.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:08.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:08.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:08.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:08.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:08.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:08.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:08.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:08.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:08.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:08.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:08.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:08.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:08.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:08.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:08.815][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:08.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:08.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:08.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:08.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:08.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:08.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:08.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:08.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.879][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:08.880][private$selectFields]
biodb.TRACE[2023-02-06 19:02:08.882][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:08.883][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:08.885][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:08.886][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.888][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.890][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.896][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.898][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:08.899][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:08.900][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.902][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.905][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.906][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:08.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.926][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-02-06 19:02:08.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:08.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:08.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:08.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:08.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:08.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:08.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:08.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:08.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:08.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.018][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.019][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.020][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.022][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.026][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.027][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.033][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.034][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.049][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.051][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.052][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.054][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.055][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.056][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:09.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.074][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-06 19:02:09.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.104][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.105][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.106][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.108][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.111][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.112][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.115][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.116][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.118][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.120][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.123][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.125][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.126][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.129][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.130][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:09.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.151][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-02-06 19:02:09.153][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:09.154][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:09.166][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:09.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:09.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:09.173][biodb::testThat]
biodb.INFO [2023-02-06 19:02:09.174][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-02-06 19:02:09.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:09.177][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:09.181][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:02:09.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:02:09.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:09.290][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:09.295][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:09.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-02-06 19:02:09.298][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:09.300][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-02-06 19:02:09.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.338][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:09.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:09.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-02-06 19:02:09.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:09.347][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-02-06 19:02:09.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.388][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:09.393][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:09.395][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-02-06 19:02:09.397][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:09.399][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-02-06 19:02:09.402][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:09.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.442][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.443][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.444][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.446][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.447][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.450][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.451][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.454][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.455][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.457][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.458][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.459][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.464][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.465][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.466][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:09.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.485][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-02-06 19:02:09.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.514][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.516][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.517][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.518][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.523][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.525][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.527][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.528][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.531][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.532][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.534][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.535][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.536][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.539][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.541][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:09.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.560][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-06 19:02:09.561][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:09.563][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:09.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:09.679][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[2023-02-06 19:02:09.683][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:09.685][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-02-06 19:02:09.687][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:09.689][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-02-06 19:02:09.693][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[2023-02-06 19:02:09.697][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:09.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-02-06 19:02:09.701][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:09.703][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-02-06 19:02:09.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:09.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:09.806][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:09.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.838][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.839][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.841][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.842][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.843][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.848][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.849][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.851][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.853][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.855][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.856][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.858][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.859][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.870][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.872][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:09.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.892][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-02-06 19:02:09.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:09.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.920][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.922][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.923][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.924][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.925][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.927][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.928][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.930][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.931][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.935][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.936][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.939][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.944][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.945][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.964][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-06 19:02:09.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:09.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:09.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:09.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:09.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:09.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:09.979][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[2023-02-06 19:02:09.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:09.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:09.991][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.992][private$selectFields]
biodb.TRACE[2023-02-06 19:02:09.994][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:09.995][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:09.996][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:09.998][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:09.999][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.002][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.003][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.005][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.007][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.010][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.014][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.015][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.017][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.035][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-02-06 19:02:10.036][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:10.037][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:10.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:10.056][biodb::testThat]
biodb.INFO [2023-02-06 19:02:10.057][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-02-06 19:02:10.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:10.060][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:02:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:02:10.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:10.170][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[2023-02-06 19:02:10.175][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:10.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-02-06 19:02:10.178][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:10.180][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-02-06 19:02:10.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.217][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[2023-02-06 19:02:10.221][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:10.223][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-02-06 19:02:10.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:10.226][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-02-06 19:02:10.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:10.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.263][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[2023-02-06 19:02:10.267][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:10.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-02-06 19:02:10.271][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:10.273][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-02-06 19:02:10.276][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:10.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.313][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.315][private$selectFields]
biodb.TRACE[2023-02-06 19:02:10.316][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:10.317][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:10.318][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.320][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.321][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.323][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.324][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.325][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.327][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.329][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.331][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.332][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.337][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.338][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:10.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.356][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-02-06 19:02:10.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.384][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.386][private$selectFields]
biodb.TRACE[2023-02-06 19:02:10.387][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:10.388][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:10.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.395][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.401][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.402][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.403][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.405][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.406][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.407][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.409][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.410][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:10.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-06 19:02:10.429][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:10.431][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:10.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:10.562][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:10.567][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:10.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-02-06 19:02:10.570][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:10.572][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-02-06 19:02:10.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:10.580][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:10.582][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-02-06 19:02:10.584][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:10.586][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-02-06 19:02:10.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:10.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:10.687][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:10.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.716][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.718][private$selectFields]
biodb.TRACE[2023-02-06 19:02:10.719][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:10.720][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:10.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.723][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.726][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.727][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.739][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.741][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.742][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.743][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.745][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.750][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.752][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:10.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.770][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-02-06 19:02:10.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.801][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.802][private$selectFields]
biodb.TRACE[2023-02-06 19:02:10.804][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:10.805][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:10.806][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.810][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.811][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.813][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.814][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.816][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.817][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.819][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.820][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.822][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.825][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.827][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.829][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:10.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.847][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-06 19:02:10.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:10.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.876][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.877][private$selectFields]
biodb.TRACE[2023-02-06 19:02:10.878][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:10.880][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:10.881][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.882][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.884][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.885][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.886][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.888][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.889][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.892][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.893][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.894][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-06 19:02:10.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.897][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.900][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.901][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-06 19:02:10.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:10.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:10.919][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-02-06 19:02:10.920][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:10.922][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:10.951][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:10.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:10.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:10.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:10.957][biodb::testThat]
biodb.INFO [2023-02-06 19:02:10.959][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-02-06 19:02:10.960][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:10.961][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:10.964][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-02-06 19:02:10.965][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:02:10.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-02-06 19:02:10.969][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:02:10.971][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:02:10.972][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:02:10.974][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:02:10.975][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:02:10.976][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:02:10.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:10.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:10.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:10.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:10.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:10.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:10.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:10.996][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-02-06 19:02:11.000][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:11.001][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:11.003][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-02-06 19:02:11.774][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-02-06 19:02:12.546][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:12.557][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-02-06 19:02:12.573][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-02-06 19:02:12.587][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-02-06 19:02:12.594][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:02:12.616][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:02:12.618][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:02:12.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:12.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:12.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:12.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:12.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:12.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:12.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:12.640][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.643][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.645][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.658][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:12.660][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:12.674][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.682][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.684][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:12.686][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:12.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.689][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.690][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:12.692][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:12.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.694][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.696][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:12.697][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:12.699][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.700][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.702][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:12.703][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:12.704][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.705][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.707][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:12.708][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:12.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.711][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.713][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:12.714][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:12.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.717][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.718][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:12.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:12.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.722][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.724][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:12.725][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:12.727][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.728][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.730][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:12.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:12.732][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.733][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:12.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:12.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:12.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:12.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:12.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:12.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:12.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:12.791][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-02-06 19:02:12.793][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-02-06 19:02:12.801][biodb::testThat]
biodb.INFO [2023-02-06 19:02:12.802][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-02-06 19:02:12.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:12.805][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:12.818][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-02-06 19:02:12.819][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-02-06 19:02:12.821][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-02-06 19:02:12.823][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-02-06 19:02:12.824][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-02-06 19:02:12.826][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:02:12.827][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:02:12.828][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:02:12.830][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:02:12.831][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:02:12.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:12.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:12.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:12.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:12.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:12.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:12.850][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[2023-02-06 19:02:12.852][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-02-06 19:02:12.855][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:12.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:12.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-02-06 19:02:13.797][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-02-06 19:02:14.575][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:14.584][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-02-06 19:02:14.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-02-06 19:02:14.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:14.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:14.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:14.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:14.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:14.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:14.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:14.625][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-02-06 19:02:14.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:14.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:14.632][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-02-06 19:02:15.428][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-02-06 19:02:16.200][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:16.210][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-02-06 19:02:16.225][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-02-06 19:02:16.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:16.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:16.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:16.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:16.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:16.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:16.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:16.247][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-02-06 19:02:16.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:16.252][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:16.254][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-02-06 19:02:17.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-02-06 19:02:17.889][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:17.899][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-02-06 19:02:17.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-02-06 19:02:17.929][private$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[2023-02-06 19:02:17.935][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:02:17.956][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-02-06 19:02:17.958][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-02-06 19:02:17.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:17.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:17.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:17.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:17.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:17.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:17.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:17.977][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:17.978][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:17.980][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:17.981][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:17.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:17.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:17.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:17.992][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:17.993][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:17.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:17.996][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:17.998][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:17.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:18.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.002][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:18.010][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:18.011][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.013][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.014][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.016][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.018][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.020][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.022][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.024][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.026][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:18.027][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:18.029][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.030][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.031][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.035][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.037][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:18.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:18.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.041][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.043][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:18.045][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:18.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.047][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:18.051][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:18.053][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.055][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:18.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:18.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:18.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:18.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:18.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:18.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:18.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:18.125][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.126][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.128][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.129][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.141][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:18.142][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:18.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.145][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.147][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:18.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:18.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.156][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:18.158][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:18.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.161][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.163][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:18.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:18.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.172][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:18.173][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:18.175][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.176][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:18.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:18.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.187][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.189][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.192][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.205][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.206][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.207][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.219][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:18.220][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:18.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.223][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.225][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:18.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:18.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.235][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.236][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.238][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.239][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.250][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:18.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:18.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.254][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:18.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:18.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.267][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:18.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:18.270][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.271][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.273][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:18.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:18.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.282][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:18.284][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:18.285][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.287][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:18.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:18.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:18.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:18.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:18.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:18.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:18.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:18.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:18.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:18.375][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.379][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.391][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:18.393][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:18.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.396][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:18.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:18.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.408][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:18.409][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:18.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.412][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:18.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:18.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.424][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:18.426][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:18.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.429][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:18.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:18.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.441][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.443][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.446][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:18.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.458][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.459][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.462][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:18.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.473][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:18.475][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:18.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.477][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:18.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:18.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.490][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.493][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.504][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:18.506][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:18.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.509][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:18.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:18.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.520][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:18.522][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:18.523][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.525][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.536][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:18.538][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:18.539][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.541][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.542][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:18.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:18.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:18.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:18.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:18.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:18.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:18.647][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-02-06 19:02:18.648][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-02-06 19:02:18.650][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-02-06 19:02:18.667][biodb::testThat]
biodb.INFO [2023-02-06 19:02:18.668][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-02-06 19:02:18.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:18.671][biodb::testThat]
biodb.INFO [2023-02-06 19:02:18.702][biodb::testThat]
biodb.INFO [2023-02-06 19:02:18.704][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-02-06 19:02:18.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:18.706][biodb::testThat]
biodb.INFO [2023-02-06 19:02:18.716][biodb::testThat]
biodb.INFO [2023-02-06 19:02:18.718][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-02-06 19:02:18.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:18.720][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:18.724][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:18.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:18.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:18.733][private$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[2023-02-06 19:02:19.607][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[2023-02-06 19:02:20.575][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:20.584][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-02-06 19:02:20.601][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-02-06 19:02:20.625][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:20.627][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:20.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:20.630][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:20.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:20.632][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:20.634][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:20.635][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:20.637][biodb::testThat]
biodb.INFO [2023-02-06 19:02:20.638][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-02-06 19:02:20.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:20.641][biodb::testThat]
biodb.ERROR[2023-02-06 19:02:20.660][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-02-06 19:02:20.680][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-02-06 19:02:20.693][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:02:20.695][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-06 19:02:20.696][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-06 19:02:20.697][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:02:20.699][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:20.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:20.701][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:20.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:20.703][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.704][FUN] Functions in observer BiodbConfig: [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 [2023-02-06 19:02:20.718][biodb::testContext]
biodb.INFO [2023-02-06 19:02:20.719][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:02:20.721][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-02-06 19:02:20.722][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:02:20.723][biodb::testContext]
biodb.INFO [2023-02-06 19:02:20.730][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:02:20.733][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:02:20.738][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:20.739][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:02:20.741][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:02:20.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.746][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:02:20.748][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:02:20.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.753][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:02:20.754][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:02:20.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.759][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:02:20.761][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:02:20.762][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:02:20.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.766][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.DEBUG[2023-02-06 19:02:20.767][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:02:20.768][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:02:20.770][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:02:20.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.775][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:02:20.776][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:02:20.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.781][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:02:20.783][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:02:20.784][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:02:20.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.789][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:02:20.791][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:02:20.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.796][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:02:20.797][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:02:20.798][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:02:20.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.804][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:02:20.805][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:02:20.806][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:02:20.808][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:02:20.809][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:02:20.811][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:02:20.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.816][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:02:20.817][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:02:20.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.822][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:02:20.824][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:02:20.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.829][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:02:20.831][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:02:20.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.836][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:02:20.838][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:02:20.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.843][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:02:20.844][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:02:20.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.849][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:02:20.851][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:02:20.855][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:02:20.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.859][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[2023-02-06 19:02:20.860][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:02:20.862][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:02:20.863][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:02:20.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:20.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:20.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:20.868][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:02:20.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.872][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-06 19:02:20.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.875][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:20.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.879][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.880][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.882][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:02:20.883][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:20.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.886][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:02:20.887][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:20.888][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.890][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.891][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:20.891][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:20.891][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:20.891][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:02:20.891][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:02:20.893][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:20.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:20.895][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:20.897][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:20.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:20.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:20.901][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.902][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.903][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:20.905][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:20.906][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.907][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.909][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:02:20.911][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.913][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:02:20.914][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.915][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:20.917][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.918][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.920][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.922][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:02:20.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:20.925][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.927][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:02:20.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:20.929][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.931][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.932][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:20.932][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:20.932][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:20.932][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:02:20.932][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:02:20.934][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:20.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:20.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:20.938][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:20.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:20.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:20.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.943][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.945][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:20.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:20.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.948][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.950][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:02:20.953][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.954][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-06 19:02:20.955][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:20.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.964][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:02:20.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:20.966][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:20.968][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:02:20.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:20.971][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.972][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:20.973][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:20.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:20.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:20.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:20.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:20.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:20.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:20.997][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:20.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:21.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:21.002][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:21.003][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:21.005][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:02:21.007][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.009][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:02:21.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:21.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:21.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:21.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:21.018][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:02:21.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:21.021][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:21.022][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:02:21.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:21.025][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:21.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.028][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:21.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:21.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:21.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:21.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:21.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:21.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:21.037][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:21.038][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:21.039][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:21.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:21.042][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:21.043][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:21.045][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:21.046][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.072][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[2023-02-06 19:02:21.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.103][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[2023-02-06 19:02:21.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.122][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[2023-02-06 19:02:21.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.128][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[2023-02-06 19:02:21.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.134][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[2023-02-06 19:02:21.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.140][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[2023-02-06 19:02:21.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.146][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[2023-02-06 19:02:21.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.154][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:02:21.156][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:02:21.157][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:02:21.159][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:02:21.161][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:02:21.163][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:02:21.165][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:02:21.167][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:02:21.169][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:02:21.171][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:02:21.173][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:02:21.175][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:02:21.177][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:02:21.179][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:02:21.181][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:02:21.183][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:02:21.185][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:02:21.187][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:02:21.189][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:02:21.191][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:02:21.193][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:02:21.195][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:02:21.197][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:02:21.199][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:02:21.201][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:02:21.202][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:02:21.204][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:02:21.206][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:02:21.208][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:02:21.210][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:02:21.212][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:02:21.214][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:02:21.216][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:02:21.218][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:02:21.220][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:02:21.222][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:02:21.224][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:02:21.226][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:02:21.228][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:02:21.230][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:02:21.232][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:02:21.234][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:02:21.236][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:02:21.238][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:02:21.240][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:02:21.242][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:02:21.244][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:02:21.246][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:02:21.248][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:02:21.250][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:02:21.252][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:02:21.254][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:02:21.256][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:02:21.258][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:02:21.260][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:02:21.262][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:02:21.264][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:02:21.266][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:02:21.267][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:02:21.269][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:02:21.271][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:02:21.273][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:02:21.275][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:02:21.277][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:02:21.279][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:02:21.281][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:02:21.283][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:02:21.285][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:02:21.287][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:02:21.289][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:02:21.291][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:02:21.294][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:02:21.295][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:02:21.297][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:02:21.299][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:02:21.301][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:02:21.303][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:02:21.305][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:02:21.308][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:02:21.310][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:02:21.312][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:02:21.314][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:02:21.315][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:02:21.318][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:02:21.320][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:02:21.321][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:21.322][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.325][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.335][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[2023-02-06 19:02:21.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.352][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[2023-02-06 19:02:21.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.370][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[2023-02-06 19:02:21.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.387][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.DEBUG[2023-02-06 19:02:21.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:21.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:21.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:21.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:21.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:21.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:21.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:21.484][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[2023-02-06 19:02:21.486][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-06 19:02:21.488][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-06 19:02:21.490][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:21.492][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:02:21.493][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:21.496][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:21.499][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.500][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-06 19:02:21.502][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:02:21.503][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:21.504][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.506][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-06 19:02:21.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-06 19:02:21.509][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-06 19:02:21.510][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:21.511][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:21.511][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:21.511][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:21.513][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:02:21.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:21.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:21.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:21.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:21.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:21.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:21.522][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:02:21.522][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-06 19:02:21.524][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:21.525][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:21.526][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:21.528][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-06 19:02:21.528][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-06 19:02:21.530][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:02:21.532][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:02:21.534][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-06 19:02:21.536][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:02:21.538][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:02:21.540][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:02:21.545][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-06 19:02:21.546][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-06 19:02:21.548][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-06 19:02:21.550][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-06 19:02:21.552][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:02:21.553][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:02:21.555][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-06 19:02:21.556][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-06 19:02:21.558][biodb::testThat]
biodb.INFO [2023-02-06 19:02:21.560][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-02-06 19:02:21.561][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:21.562][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:21.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-06 19:02:21.573][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:21.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:21.576][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-02-06 19:02:22.435][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-02-06 19:02:23.392][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:23.402][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-02-06 19:02:23.418][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-02-06 19:02:23.427][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:23.432][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:23.433][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:23.435][private$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[2023-02-06 19:02:24.201][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[2023-02-06 19:02:24.942][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:24.952][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-02-06 19:02:24.968][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-02-06 19:02:24.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:24.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:24.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:24.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:24.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:24.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:24.988][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.DEBUG[2023-02-06 19:02:24.990][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[2023-02-06 19:02:24.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:24.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:24.998][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:02:25.759][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:02:26.574][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:26.583][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-02-06 19:02:26.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-02-06 19:02:26.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.659][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:26.664][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:26.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-02-06 19:02:26.667][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:26.669][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-02-06 19:02:26.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.687][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:26.692][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:26.693][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-02-06 19:02:26.695][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:26.697][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-02-06 19:02:26.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:26.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:26.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-02-06 19:02:26.740][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:26.741][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-02-06 19:02:26.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.760][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:26.764][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:26.765][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-02-06 19:02:26.767][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:26.769][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-02-06 19:02:26.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:26.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:26.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:26.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:26.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:26.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:26.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:26.787][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:26.792][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:26.793][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:26.796][private$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[2023-02-06 19:02:28.026][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[2023-02-06 19:02:28.803][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:28.812][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-02-06 19:02:28.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-02-06 19:02:28.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:28.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:28.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:28.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:28.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:28.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:28.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:02:28.852][biodb::testThat]
biodb.INFO [2023-02-06 19:02:28.853][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-02-06 19:02:28.854][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:28.856][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:28.860][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[2023-02-06 19:02:28.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:28.866][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:28.869][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:02:29.642][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:02:30.376][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:30.406][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-02-06 19:02:30.423][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-02-06 19:02:30.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:30.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:30.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:30.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:30.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:30.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:30.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:30.447][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:30.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:30.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:30.456][private$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[2023-02-06 19:02:31.261][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[2023-02-06 19:02:32.041][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:32.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-02-06 19:02:32.065][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-02-06 19:02:32.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:32.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:02:32.088][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:02:32.089][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-06 19:02:32.091][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-06 19:02:32.092][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:02:32.093][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.096][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.098][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:02:32.104][biodb::testContext]
biodb.INFO [2023-02-06 19:02:32.105][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:02:32.107][biodb::testContext] Test context - Test web services
biodb.INFO [2023-02-06 19:02:32.108][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:02:32.109][biodb::testContext]
biodb.INFO [2023-02-06 19:02:32.116][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:02:32.118][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:02:32.122][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:32.124][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:02:32.125][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:02:32.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.131][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:02:32.132][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:02:32.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.137][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:02:32.139][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:02:32.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.144][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:02:32.145][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:02:32.147][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:02:32.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.152][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:02:32.153][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:02:32.155][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:02:32.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.160][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:02:32.161][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:02:32.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.165][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[2023-02-06 19:02:32.167][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:02:32.168][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:02:32.169][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:02:32.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.175][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:02:32.176][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:02:32.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.181][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:02:32.183][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:02:32.184][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:02:32.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.189][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:02:32.191][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:02:32.192][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:02:32.194][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:02:32.195][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:02:32.197][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:02:32.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.202][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:02:32.203][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:02:32.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.208][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:02:32.210][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:02:32.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.215][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:02:32.216][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:02:32.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.221][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:02:32.223][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:02:32.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.228][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:02:32.229][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:02:32.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.235][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:02:32.236][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:02:32.240][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:02:32.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.245][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:02:32.247][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:02:32.248][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:02:32.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.254][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:02:32.256][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.257][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-06 19:02:32.259][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.260][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:32.262][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.263][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.267][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:02:32.269][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:32.270][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.272][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:02:32.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:32.274][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.276][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.277][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:32.277][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:32.277][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:32.277][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:02:32.277][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:02:32.279][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:32.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:32.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.287][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.288][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.290][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:32.291][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:32.292][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.294][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.295][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:02:32.298][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.299][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:02:32.301][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.302][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:32.303][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.305][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.306][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.309][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:02:32.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:32.312][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.313][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:02:32.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:32.316][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.318][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.319][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:32.319][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:32.319][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:32.319][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:02:32.319][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:02:32.320][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:32.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.324][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:32.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.330][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:32.332][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:32.334][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.335][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.337][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:02:32.339][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.341][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-06 19:02:32.342][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.344][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:32.345][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.348][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.349][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.351][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:02:32.352][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:32.354][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.364][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:02:32.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:32.374][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.375][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.377][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.378][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:32.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:32.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.387][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.388][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.390][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:32.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:32.392][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.394][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.396][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:02:32.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.400][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:02:32.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.402][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:32.404][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.410][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:02:32.411][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:32.412][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.414][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:02:32.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:32.417][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.420][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.421][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:32.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.425][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:32.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.429][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.431][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.432][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:32.433][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:32.435][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.436][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:32.438][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:32.439][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.460][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[2023-02-06 19:02:32.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.506][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[2023-02-06 19:02:32.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.513][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[2023-02-06 19:02:32.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.532][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[2023-02-06 19:02:32.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.546][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.DEBUG[2023-02-06 19:02:32.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.552][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.DEBUG[2023-02-06 19:02:32.553][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:02:32.556][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:02:32.558][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:02:32.560][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:02:32.562][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:02:32.564][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:02:32.566][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:02:32.568][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:02:32.570][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:02:32.572][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:02:32.574][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:02:32.576][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:02:32.578][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:02:32.580][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:02:32.582][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:02:32.584][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:02:32.586][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:02:32.588][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:02:32.590][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:02:32.592][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:02:32.594][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:02:32.596][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:02:32.598][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:02:32.600][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:02:32.602][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:02:32.604][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:02:32.606][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:02:32.608][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:02:32.610][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:02:32.612][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:02:32.614][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:02:32.616][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:02:32.618][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:02:32.620][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:02:32.622][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:02:32.624][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:02:32.626][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:02:32.628][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:02:32.630][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:02:32.632][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:02:32.634][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:02:32.636][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:02:32.638][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:02:32.640][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:02:32.642][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:02:32.644][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:02:32.646][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:02:32.648][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:02:32.650][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:02:32.652][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:02:32.654][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:02:32.656][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:02:32.658][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:02:32.660][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:02:32.662][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:02:32.664][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:02:32.666][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:02:32.668][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:02:32.670][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:02:32.672][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:02:32.674][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:02:32.676][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:02:32.678][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:02:32.680][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:02:32.682][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:02:32.684][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:02:32.686][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:02:32.688][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:02:32.690][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:02:32.692][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:02:32.694][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:02:32.697][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:02:32.699][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:02:32.701][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:02:32.703][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:02:32.705][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:02:32.707][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:02:32.709][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:02:32.711][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:02:32.713][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:02:32.716][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:02:32.718][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:02:32.720][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:02:32.722][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:02:32.724][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:02:32.726][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:32.727][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.730][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.741][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[2023-02-06 19:02:32.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.786][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[2023-02-06 19:02:32.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.840][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[2023-02-06 19:02:32.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.849][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[2023-02-06 19:02:32.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.875][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[2023-02-06 19:02:32.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:32.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:32.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:32.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:32.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:32.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:32.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:32.895][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-06 19:02:32.897][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-06 19:02:32.900][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.901][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.902][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.904][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:32.905][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.908][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.910][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-06 19:02:32.911][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:02:32.912][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:32.914][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.915][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-06 19:02:32.917][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-06 19:02:32.918][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-06 19:02:32.920][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:32.921][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:32.921][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:32.921][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:32.923][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:02:32.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:32.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:32.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:32.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:32.932][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:02:32.932][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-06 19:02:32.934][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:32.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:32.936][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:32.938][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-06 19:02:32.938][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-06 19:02:32.939][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:02:32.942][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:02:32.944][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-06 19:02:32.946][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:02:32.948][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:02:32.950][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:02:32.954][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-06 19:02:32.956][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-06 19:02:32.957][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-06 19:02:32.959][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-06 19:02:32.961][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:02:32.962][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:02:32.964][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-06 19:02:32.966][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-06 19:02:32.967][biodb::testThat]
biodb.INFO [2023-02-06 19:02:32.969][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-02-06 19:02:32.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:32.972][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:32.976][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-06 19:02:32.981][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:32.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-02-06 19:02:32.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:32.987][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-02-06 19:02:32.992][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[2023-02-06 19:02:32.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:32.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:33.000][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-02-06 19:02:33.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-02-06 19:02:35.536][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:35.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-02-06 19:02:35.560][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-02-06 19:02:35.568][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:02:35.570][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-06 19:02:35.572][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-06 19:02:35.573][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:02:35.574][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:35.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:35.576][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.579][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:02:35.585][biodb::testContext]
biodb.INFO [2023-02-06 19:02:35.586][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:02:35.587][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-02-06 19:02:35.588][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:02:35.590][biodb::testContext]
biodb.INFO [2023-02-06 19:02:35.596][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:02:35.598][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:02:35.602][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:35.603][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:02:35.605][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:02:35.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.610][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:02:35.611][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:02:35.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.616][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:02:35.617][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:02:35.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.622][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:02:35.624][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:02:35.625][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:02:35.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.630][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:02:35.631][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:02:35.633][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:02:35.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.638][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:02:35.639][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:02:35.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.644][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:02:35.645][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:02:35.647][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:02:35.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.651][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:02:35.653][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:02:35.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.658][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:02:35.659][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:02:35.660][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:02:35.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.665][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:02:35.667][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:02:35.668][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:02:35.669][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:02:35.671][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:02:35.672][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:02:35.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.677][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:02:35.678][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:02:35.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.683][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:02:35.685][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:02:35.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.690][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:02:35.691][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:02:35.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.711][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:02:35.713][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:02:35.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.718][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:02:35.719][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:02:35.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.724][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:02:35.725][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:02:35.729][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:02:35.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.734][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:02:35.735][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:02:35.736][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:02:35.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.741][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:02:35.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.745][self$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[2023-02-06 19:02:35.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:35.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.751][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.753][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.754][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:02:35.755][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:35.757][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.758][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:02:35.759][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:35.760][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:02:35.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:35.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:35.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.773][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.774][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:35.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:35.777][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.778][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.779][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:02:35.782][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.783][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:02:35.784][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.786][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:35.787][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.788][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.789][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.791][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.792][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:02:35.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:35.795][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.796][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:02:35.797][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:35.799][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.801][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:35.801][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:35.801][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:35.801][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:02:35.801][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:02:35.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:35.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.806][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:35.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.810][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.811][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.812][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:35.813][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:35.815][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.816][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.818][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:02:35.820][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.821][self$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[2023-02-06 19:02:35.823][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.824][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:35.825][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.826][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.828][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.829][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.830][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:02:35.831][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:35.833][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.834][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:02:35.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:35.837][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.838][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.839][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:35.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.844][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:35.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.848][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.849][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.850][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:35.851][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:35.853][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.854][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.855][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:02:35.858][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:02:35.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:35.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.866][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.868][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:02:35.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:35.871][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.872][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:02:35.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:35.875][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:35.877][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.879][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:02:35.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:35.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:35.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:35.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:35.887][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.889][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:35.890][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:35.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:35.892][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:02:35.894][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:35.895][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.932][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[2023-02-06 19:02:35.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:35.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:35.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:35.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:35.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:35.998][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:02:36.000][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:02:36.002][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:02:36.004][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:02:36.005][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:02:36.007][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:02:36.009][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:02:36.011][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:02:36.013][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:02:36.015][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:02:36.017][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:02:36.018][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:02:36.020][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:02:36.022][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:02:36.024][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:02:36.026][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:02:36.028][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:02:36.030][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:02:36.032][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:02:36.034][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:02:36.035][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:02:36.037][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:02:36.039][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:02:36.041][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:02:36.043][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:02:36.045][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:02:36.047][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:02:36.049][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:02:36.051][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:02:36.053][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:02:36.055][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:02:36.057][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:02:36.059][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:02:36.061][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:02:36.063][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:02:36.065][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:02:36.067][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:02:36.069][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:02:36.071][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:02:36.072][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:02:36.074][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:02:36.076][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:02:36.078][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:02:36.080][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:02:36.082][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:02:36.084][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:02:36.086][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:02:36.088][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:02:36.090][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:02:36.092][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:02:36.094][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:02:36.104][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:02:36.107][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:02:36.109][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:02:36.111][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:02:36.113][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:02:36.115][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:02:36.117][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:02:36.119][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:02:36.120][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:02:36.122][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:02:36.124][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:02:36.126][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:02:36.128][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:02:36.130][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:02:36.132][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:02:36.134][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:02:36.136][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:02:36.138][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:02:36.140][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:02:36.142][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:02:36.144][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:02:36.145][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:02:36.147][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:02:36.149][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:02:36.151][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:02:36.153][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:02:36.155][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:02:36.157][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:02:36.159][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:02:36.161][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:02:36.163][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:02:36.164][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:02:36.167][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:02:36.169][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:02:36.170][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:02:36.171][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.173][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.191][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[2023-02-06 19:02:36.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.276][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[2023-02-06 19:02:36.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.301][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.DEBUG[2023-02-06 19:02:36.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:02:36.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.318][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[2023-02-06 19:02:36.320][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-06 19:02:36.321][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-06 19:02:36.324][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:36.325][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:02:36.327][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:36.328][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:02:36.329][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:36.331][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:02:36.332][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:36.333][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-06 19:02:36.335][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:02:36.336][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:02:36.337][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:36.339][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-06 19:02:36.340][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-06 19:02:36.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-06 19:02:36.343][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:02:36.344][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:02:36.344][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:02:36.344][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:02:36.346][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:02:36.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:36.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:36.349][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:02:36.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:02:36.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:02:36.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:02:36.354][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:02:36.354][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-06 19:02:36.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:02:36.357][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:02:36.358][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:02:36.360][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-06 19:02:36.360][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-06 19:02:36.362][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:02:36.364][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:02:36.366][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-06 19:02:36.368][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:02:36.370][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:02:36.372][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:02:36.376][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-06 19:02:36.378][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-06 19:02:36.379][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-06 19:02:36.381][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-06 19:02:36.383][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:02:36.384][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:02:36.386][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-06 19:02:36.388][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-06 19:02:36.389][biodb::testThat]
biodb.INFO [2023-02-06 19:02:36.391][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-02-06 19:02:36.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:36.393][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:36.398][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-06 19:02:36.402][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:36.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-02-06 19:02:36.406][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:36.408][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-02-06 19:02:36.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-06 19:02:36.416][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:36.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-02-06 19:02:36.420][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:36.421][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-02-06 19:02:36.425][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-02-06 19:02:36.427][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:02:36.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-02-06 19:02:36.430][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:02:36.432][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:02:36.433][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:02:36.435][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-06 19:02:36.436][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:02:36.437][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:02:36.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:36.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:36.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:36.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:36.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:36.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:36.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:36.456][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-02-06 19:02:36.460][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:36.461][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:36.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-02-06 19:02:37.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-02-06 19:02:38.677][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:38.686][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-02-06 19:02:38.701][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-02-06 19:02:38.715][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-02-06 19:02:38.720][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:02:38.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:02:38.742][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-06 19:02:38.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:38.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:38.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:38.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:38.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:38.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:38.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:38.762][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.764][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.767][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.778][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:38.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:38.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.782][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.784][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-06 19:02:38.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-06 19:02:38.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.794][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:38.795][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:38.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.798][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.800][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:38.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:38.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.810][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:02:38.812][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:02:38.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.815][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.817][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:02:38.819][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:02:38.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.822][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.824][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:38.826][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:38.827][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.829][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.831][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:38.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:38.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.841][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:38.843][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:38.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.846][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.849][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-06 19:02:38.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.859][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:38.861][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:38.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.864][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:38.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:38.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.875][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:38.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:38.879][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.880][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:38.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:38.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.892][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:38.894][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:38.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.897][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.899][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-06 19:02:38.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-06 19:02:38.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.909][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:38.911][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:38.912][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.914][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:02:38.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:02:38.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:38.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:38.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:38.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:38.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:38.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:38.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:38.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:38.989][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-02-06 19:02:38.991][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:02:38.993][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-06 19:02:38.994][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-06 19:02:38.996][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:02:38.997][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:38.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:39.000][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:39.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:39.002][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:39.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
>
> proc.time()
user system elapsed
32.462 0.973 109.778
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.841 | 0.206 | 5.223 | |
| ChebiEntry | 0.508 | 0.004 | 0.634 | |