| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-27 02:34:30 -0000 (Mon, 27 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" | 4259 |
| 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 179/2169 | 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: 2023-02-24 07:50:00 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 07:55:04 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 303.7 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 2.94 0.158 6.518
* 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 [2023-02-24 07:51:02.879][biodb::testContext]
biodb.INFO [2023-02-24 07:51:02.882][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:51:02.883][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-02-24 07:51:02.885][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:51:02.886][biodb::testContext]
biodb.INFO [2023-02-24 07:51:02.907][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:51:02.910][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-24 07:51:02.920][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:51:02.921][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-24 07:51:02.923][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-24 07:51:02.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:02.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:02.928][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-24 07:51:02.957][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-24 07:51:02.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:02.961][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[2023-02-24 07:51:02.962][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-24 07:51:02.964][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-24 07:51:02.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:02.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:02.969][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-24 07:51:02.971][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-24 07:51:02.972][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-24 07:51:02.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:02.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:02.978][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-24 07:51:02.979][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-24 07:51:02.981][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-24 07:51:02.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:02.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:02.986][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-24 07:51:02.988][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-24 07:51:02.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:02.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:02.993][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-24 07:51:02.995][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-24 07:51:02.996][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-24 07:51:02.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:02.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.001][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-24 07:51:03.003][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-24 07:51:03.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.008][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-24 07:51:03.010][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-24 07:51:03.011][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-24 07:51:03.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.017][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:51:03.018][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-24 07:51:03.020][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-24 07:51:03.021][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-24 07:51:03.023][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-24 07:51:03.024][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-24 07:51:03.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.029][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-24 07:51:03.031][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-24 07:51:03.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.036][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-24 07:51:03.038][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-24 07:51:03.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.043][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-24 07:51:03.045][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-24 07:51:03.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.050][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-24 07:51:03.051][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-24 07:51:03.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.057][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-24 07:51:03.058][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-24 07:51:03.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.064][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:51:03.065][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-24 07:51:03.070][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-24 07:51:03.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.075][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-24 07:51:03.076][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-24 07:51:03.078][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-24 07:51:03.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.087][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-24 07:51:03.148][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.170][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-24 07:51:03.172][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.173][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:51:03.174][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.176][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.177][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.178][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.180][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:51:03.181][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:51:03.182][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.184][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-24 07:51:03.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:51:03.186][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.188][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.189][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:51:03.189][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:51:03.189][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:51:03.189][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:51:03.189][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:51:03.190][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:51:03.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.194][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:51:03.195][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.199][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.200][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:51:03.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:51:03.203][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.204][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.206][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-24 07:51:03.208][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.210][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:51:03.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:51:03.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.219][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:51:03.220][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:51:03.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.223][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-24 07:51:03.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:51:03.226][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.228][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:51:03.228][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:51:03.228][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:51:03.228][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:51:03.228][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:51:03.230][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:51:03.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.233][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:51:03.235][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.237][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.239][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.240][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:51:03.241][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:51:03.242][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.244][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.245][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-24 07:51:03.248][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.249][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-24 07:51:03.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:51:03.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.256][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.257][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.258][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:51:03.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:51:03.261][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.262][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-24 07:51:03.264][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:51:03.265][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.268][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.269][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:51:03.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.273][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:51:03.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.276][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.278][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.279][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:51:03.280][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:51:03.281][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.283][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.284][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-24 07:51:03.287][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.288][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:51:03.289][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.291][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:51:03.292][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.293][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.295][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.297][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:51:03.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:51:03.300][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.301][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-24 07:51:03.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:51:03.304][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.307][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.308][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:51:03.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:51:03.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.316][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.317][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.318][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:51:03.319][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:51:03.321][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.322][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:51:03.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:51:03.328][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.354][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.DEBUG[2023-02-24 07:51:03.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.372][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.DEBUG[2023-02-24 07:51:03.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.378][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[2023-02-24 07:51:03.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.396][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[2023-02-24 07:51:03.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.420][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.DEBUG[2023-02-24 07:51:03.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.432][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[2023-02-24 07:51:03.433][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-24 07:51:03.439][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-24 07:51:03.441][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-24 07:51:03.443][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-24 07:51:03.445][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:51:03.447][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-24 07:51:03.449][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-24 07:51:03.451][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-24 07:51:03.453][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-24 07:51:03.455][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-24 07:51:03.456][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:51:03.458][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-24 07:51:03.460][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-24 07:51:03.470][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-24 07:51:03.472][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-24 07:51:03.474][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-24 07:51:03.476][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-24 07:51:03.478][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-24 07:51:03.480][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:51:03.481][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-24 07:51:03.483][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-24 07:51:03.485][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-24 07:51:03.487][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-24 07:51:03.489][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-24 07:51:03.491][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-24 07:51:03.493][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-24 07:51:03.495][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-24 07:51:03.497][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-24 07:51:03.499][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-24 07:51:03.501][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-24 07:51:03.503][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-24 07:51:03.505][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-24 07:51:03.507][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-24 07:51:03.509][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-24 07:51:03.511][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-24 07:51:03.512][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-24 07:51:03.514][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-24 07:51:03.516][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-24 07:51:03.518][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-24 07:51:03.520][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-24 07:51:03.522][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-24 07:51:03.524][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-24 07:51:03.526][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-24 07:51:03.528][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-24 07:51:03.530][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-24 07:51:03.532][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-24 07:51:03.534][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-24 07:51:03.536][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-24 07:51:03.538][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-24 07:51:03.540][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-24 07:51:03.542][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-24 07:51:03.543][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-24 07:51:03.545][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-24 07:51:03.547][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-24 07:51:03.549][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-24 07:51:03.551][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-24 07:51:03.553][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-24 07:51:03.555][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-24 07:51:03.557][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-24 07:51:03.559][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-24 07:51:03.565][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-24 07:51:03.567][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-24 07:51:03.569][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-24 07:51:03.571][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-24 07:51:03.572][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-24 07:51:03.574][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-24 07:51:03.576][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:51:03.578][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:51:03.580][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-24 07:51:03.582][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-24 07:51:03.584][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-24 07:51:03.586][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-24 07:51:03.588][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-24 07:51:03.590][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-24 07:51:03.592][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-24 07:51:03.594][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-24 07:51:03.596][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-24 07:51:03.598][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-24 07:51:03.600][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-24 07:51:03.602][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-24 07:51:03.604][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-24 07:51:03.606][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-24 07:51:03.608][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-24 07:51:03.616][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-24 07:51:03.618][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:51:03.622][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:51:03.624][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.626][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.650][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[2023-02-24 07:51:03.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.751][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[2023-02-24 07:51:03.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:03.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.768][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[2023-02-24 07:51:03.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:51:03.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.777][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[2023-02-24 07:51:03.779][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-24 07:51:03.800][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-24 07:51:03.803][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.805][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:51:03.809][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.810][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.812][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.813][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-24 07:51:03.814][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-24 07:51:03.816][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:51:03.817][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.818][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-24 07:51:03.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-24 07:51:03.821][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-24 07:51:03.823][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-24 07:51:03.824][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:51:03.824][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:51:03.824][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:51:03.825][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-24 07:51:03.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:51:03.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:51:03.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:51:03.833][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:51:03.835][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:51:03.835][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-24 07:51:03.836][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:51:03.838][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:51:03.839][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-24 07:51:03.840][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-24 07:51:03.840][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-24 07:51:03.849][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:51:03.851][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:51:03.854][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-24 07:51:03.856][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:51:03.858][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:51:03.860][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:51:03.893][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-24 07:51:03.895][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-24 07:51:03.901][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-24 07:51:03.907][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-24 07:51:03.913][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:51:03.915][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:51:03.917][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-24 07:51:03.918][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-24 07:51:03.941][biodb::testThat]
biodb.INFO [2023-02-24 07:51:03.942][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-02-24 07:51:03.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:03.945][biodb::testThat]
biodb.TRACE[2023-02-24 07:51:03.951][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-02-24 07:51:03.958][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:51:03.963][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:51:03.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:03.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:03.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:03.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:03.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:03.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:03.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:51:04.012][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.013][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.016][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.044][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.046][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.047][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.049][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.086][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.096][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.098][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.100][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.111][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:04.112][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:04.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.115][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:04.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:04.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.128][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.131][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.142][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.144][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.145][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.146][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.171][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:51:04.173][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.176][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.177][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:51:04.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.187][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.188][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.191][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.202][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.204][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.205][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.206][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.218][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:51:04.219][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.220][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.222][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.224][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:51:04.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.233][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.234][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.237][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:04.354][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-02-24 07:51:04.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:04.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:04.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:04.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.425][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-24 07:51:04.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-24 07:51:04.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-24 07:51:04.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-24 07:51:04.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-24 07:51:04.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-24 07:51:04.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-24 07:51:04.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-24 07:51:04.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.589][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.590][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.593][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:04.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:04.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.630][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:04.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.663][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.664][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.665][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.667][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:04.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.683][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.699][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.701][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.703][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:04.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.773][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.775][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.776][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.778][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:04.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.811][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.813][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.815][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:04.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.831][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.848][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.849][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.851][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.852][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.853][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:04.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.868][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.874][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.880][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.885][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.886][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.889][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.890][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:04.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.905][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.911][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.916][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.922][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.923][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.926][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:04.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.942][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.958][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.960][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.962][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:04.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:04.996][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.997][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:04.999][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.000][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.035][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.037][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.061][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.064][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.065][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.073][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:05.074][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:05.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.077][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.085][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:05.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:05.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.089][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.101][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.108][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.113][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:05.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:05.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.125][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.132][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:05.134][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:05.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.137][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.144][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:05.146][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:05.147][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.149][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.156][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-02-24 07:51:05.158][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:05.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.161][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.168][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.173][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:05.182][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:05.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.185][ef$get] fields variable is a list.
biodb.INFO [2023-02-24 07:51:05.193][biodb::testThat]
biodb.INFO [2023-02-24 07:51:05.195][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-02-24 07:51:05.196][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:05.197][biodb::testThat]
biodb.DEBUG[2023-02-24 07:51:05.217][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-02-24 07:51:05.227][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:51:05.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-02-24 07:51:05.234][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:51:05.236][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-02-24 07:51:05.238][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:51:05.296][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:51:05.298][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:51:05.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:05.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:05.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:05.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:05.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:05.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:05.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:51:05.317][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.319][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.321][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.363][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:05.365][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:05.366][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.367][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.369][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:05.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:05.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.378][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:05.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:05.381][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.382][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.384][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:05.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:05.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.393][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.395][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.398][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:05.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:05.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.409][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.410][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.413][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:05.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.424][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:05.426][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:05.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.429][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.430][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:05.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:05.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.440][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:51:05.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:05.443][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.444][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:51:05.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:05.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:05.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:05.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.460][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:05.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.471][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.474][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.475][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.486][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:51:05.488][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:05.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.491][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.492][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:51:05.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:05.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.502][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:05.503][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:05.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.506][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.508][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:05.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:05.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:05.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:05.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:05.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:05.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:05.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:05.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:05.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:05.577][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-02-24 07:51:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-02-24 07:51:05.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-02-24 07:51:05.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-02-24 07:51:05.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-02-24 07:51:05.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-02-24 07:51:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-02-24 07:51:05.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-24 07:51:05.603][biodb::testThat]
biodb.INFO [2023-02-24 07:51:05.604][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-02-24 07:51:05.605][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:05.607][biodb::testThat]
biodb.TRACE[2023-02-24 07:51:05.610][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.615][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:05.624][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-02-24 07:51:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:05.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:05.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:05.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:05.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:05.681][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-02-24 07:51:05.697][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-24 07:51:05.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:51:05.747][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-02-24 07:51:05.749][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:51:05.750][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-02-24 07:51:05.782][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[2023-02-24 07:51:05.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:05.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:05.790][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:51:08.501][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:51:10.784][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2023-02-24 07:51:10.794][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-02-24 07:51:10.802][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-02-24 07:51:10.840][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-02-24 07:51:10.848][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-02-24 07:51:10.870][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:10.872][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:10.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:10.875][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:10.877][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:10.878][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:10.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:10.881][ef$get] fields variable is a list.
biodb.INFO [2023-02-24 07:51:10.884][biodb::testThat]
biodb.INFO [2023-02-24 07:51:10.886][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-02-24 07:51:10.887][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:10.889][biodb::testThat]
biodb.TRACE[2023-02-24 07:51:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:10.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:10.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:10.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:10.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:10.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:10.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:10.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:10.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:10.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:10.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:10.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:11.066][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[2023-02-24 07:51:11.071][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:51:11.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-24 07:51:11.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:51:11.077][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-02-24 07:51:11.101][biodb::testThat]
biodb.INFO [2023-02-24 07:51:11.103][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-02-24 07:51:11.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:11.106][biodb::testThat]
biodb.TRACE[2023-02-24 07:51:11.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:11.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:11.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:11.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:11.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.189][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-24 07:51:11.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-24 07:51:11.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-24 07:51:11.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-24 07:51:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:11.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:11.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:11.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:11.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:11.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-24 07:51:11.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.310][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-24 07:51:11.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-24 07:51:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:11.318][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-24 07:51:11.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-24 07:51:11.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:11.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-24 07:51:11.334][biodb::testThat]
biodb.INFO [2023-02-24 07:51:11.336][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-02-24 07:51:11.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:11.339][biodb::testThat]
biodb.INFO [2023-02-24 07:51:11.350][biodb::testThat]
biodb.INFO [2023-02-24 07:51:11.352][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-02-24 07:51:11.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:11.356][biodb::testThat]
biodb.INFO [2023-02-24 07:51:11.365][biodb::testThat]
biodb.INFO [2023-02-24 07:51:11.367][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-02-24 07:51:11.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:11.370][biodb::testThat]
biodb.DEBUG[2023-02-24 07:51:11.376][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-02-24 07:51:12.640][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-02-24 07:51:16.797][biodb::testThat]
biodb.INFO [2023-02-24 07:51:16.799][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-02-24 07:51:16.801][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:16.803][biodb::testThat]
biodb.DEBUG[2023-02-24 07:51:17.982][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[2023-02-24 07:51:19.143][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:19.146][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:19.148][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:19.208][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:19.210][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:19.212][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:19.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:19.215][ef$get] fields variable is a list.
biodb.INFO [2023-02-24 07:51:19.218][biodb::testThat]
biodb.INFO [2023-02-24 07:51:19.220][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-02-24 07:51:19.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:51:19.223][biodb::testThat]
biodb.TRACE[2023-02-24 07:51:19.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:19.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:19.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:19.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:19.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:19.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:19.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:19.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:19.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:19.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:19.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:19.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2023-02-24 07:51:19.400][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2023-02-24 07:51:19.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:19.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:19.448][private$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[2023-02-24 07:51:20.705][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[2023-02-24 07:51:21.948][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:51:21.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-02-24 07:51:21.973][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-02-24 07:51:22.097][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[2023-02-24 07:51:22.102][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:51:22.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-24 07:51:22.106][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:51:22.108][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-02-24 07:51:22.156][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-24 07:51:22.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-24 07:51:22.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:22.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:22.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:22.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:22.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:22.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:22.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:22.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:22.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:22.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:22.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:22.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:22.262][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[2023-02-24 07:51:22.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:22.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:22.271][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:51:23.436][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:51:25.411][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:51:25.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-02-24 07:51:25.437][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-02-24 07:51:25.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:25.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:25.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:25.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:25.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:25.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:25.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:25.461][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-02-24 07:51:25.542][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:51:25.544][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-02-24 07:51:25.546][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:51:25.548][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:51:25.549][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:51:25.551][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:51:25.552][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:51:25.553][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:51:25.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:25.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:25.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:25.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:25.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:25.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:25.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:25.574][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-02-24 07:51:25.578][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:25.579][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:25.581][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-02-24 07:51:26.749][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-02-24 07:51:27.894][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:51:27.904][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-02-24 07:51:27.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-02-24 07:51:27.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-02-24 07:51:27.939][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:51:27.977][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:51:27.978][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:51:27.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:27.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:27.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:27.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:27.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:27.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:27.996][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.TRACE[2023-02-24 07:51:27.999][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.000][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.003][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.016][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:28.017][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:28.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.020][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.022][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:51:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:51:28.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.032][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:28.034][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:28.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.036][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.039][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:51:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:51:28.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.048][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:28.050][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:28.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.053][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:51:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:51:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.065][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:28.066][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:28.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.069][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:51:28.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:51:28.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:28.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:51:28.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.085][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.087][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:51:28.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.094][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.095][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.097][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:51:28.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.109][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:28.111][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:28.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.114][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:28.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:51:28.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.125][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:28.127][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:28.128][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.129][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:51:28.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:51:28.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.141][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:51:28.143][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:28.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.146][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.148][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:51:28.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:51:28.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.157][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:28.164][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:28.166][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.167][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:51:28.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:51:28.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:28.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:28.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:28.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:28.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:51:28.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:51:28.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:51:28.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:51:28.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:28.269][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-02-24 07:51:28.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:28.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:28.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:28.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:28.304][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:51:28.318][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:28.320][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:28.323][private$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[2023-02-24 07:51:52.051][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2023-02-24 07:51:52.057][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-24 07:51:52.059][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-24 07:51:52.061][getBaseUrlRequestResult] Using base::url() 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[2023-02-24 07:51:53.703][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:51:53.718][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-02-24 07:51:53.737][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-02-24 07:51:53.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:53.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:53.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:53.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:53.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:53.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:53.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:51:53.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:53.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:53.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:53.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:53.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:53.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:53.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:53.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:53.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:53.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:53.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:53.829][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[2023-02-24 07:51:53.835][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:53.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:53.840][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:51:55.057][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:51:57.479][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:51:57.489][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-02-24 07:51:57.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-02-24 07:51:57.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:51:57.574][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:51:57.576][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-24 07:51:57.578][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:51:57.580][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-24 07:51:57.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:57.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:57.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:57.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:57.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:57.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:57.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:51:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:57.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:57.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:57.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:57.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:57.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:51:57.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:57.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:51:57.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:51:57.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:51:57.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:57.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:57.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:57.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:57.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:57.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:57.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:57.652][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-02-24 07:51:57.654][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:51:57.656][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-02-24 07:51:57.658][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:51:57.659][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:51:57.675][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:51:57.676][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:51:57.678][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:51:57.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:51:57.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:51:57.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:51:57.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:51:57.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:51:57.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:51:57.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:51:57.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:51:57.715][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-02-24 07:51:57.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:51:57.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:51:57.722][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-02-24 07:51:58.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-02-24 07:52:01.776][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:01.786][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-02-24 07:52:01.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-02-24 07:52:01.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-02-24 07:52:01.819][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:01.841][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:01.843][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:01.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:01.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:01.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:01.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:01.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:01.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:01.859][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.TRACE[2023-02-24 07:52:01.862][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:01.864][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:01.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.867][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:01.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:01.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.877][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:01.879][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:01.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.882][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.883][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:01.885][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:01.900][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.901][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.903][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:01.905][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:01.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.907][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:01.915][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:01.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.918][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.921][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:01.922][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:01.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.925][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.927][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:01.929][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:01.931][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.932][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.934][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:01.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:01.937][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.938][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.940][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:01.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:01.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.945][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:01.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:01.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.959][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:01.960][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:01.962][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.964][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:01.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.976][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:01.978][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:01.979][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.981][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:01.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:01.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:01.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:01.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:01.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:01.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:01.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:02.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:02.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:02.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:02.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:02.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:02.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:02.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:02.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:02.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:02.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:02.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:02.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:02.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:02.051][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-02-24 07:52:02.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:02.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:02.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:02.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:02.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:02.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:02.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:02.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:02.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:02.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:02.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:02.104][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-02-24 07:52:02.106][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:02.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-02-24 07:52:02.110][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:02.112][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:02.114][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:02.115][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:02.117][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:02.118][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:02.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:02.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:02.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:02.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:02.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:02.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:02.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:02.140][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-02-24 07:52:02.144][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:02.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:02.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-02-24 07:52:04.246][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-02-24 07:52:06.392][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:06.401][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-02-24 07:52:06.415][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-02-24 07:52:06.428][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-02-24 07:52:06.434][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:06.455][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:06.457][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:06.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:06.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:06.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:06.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:06.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:06.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:06.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:06.476][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.477][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.480][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.491][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:06.492][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:06.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.495][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.496][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:06.498][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:06.499][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.500][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:06.504][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:06.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.506][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.508][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:06.510][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:06.511][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.512][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.514][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:06.515][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:06.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.518][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.520][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:06.521][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.524][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.525][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:06.527][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:06.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.529][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.531][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:06.533][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:06.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.535][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:06.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:06.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.547][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:06.549][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:06.550][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.551][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.553][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:06.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:06.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.577][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:06.578][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:06.580][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.581][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:06.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:06.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:06.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:06.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:06.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:06.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:06.642][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-02-24 07:52:06.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:06.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:06.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:06.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:06.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:06.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:06.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:06.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:06.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:06.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:06.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:06.687][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-02-24 07:52:06.689][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:06.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-02-24 07:52:06.693][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:06.694][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:06.696][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:06.697][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:06.698][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:06.700][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:06.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:06.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:06.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:06.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:06.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:06.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:06.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:06.720][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-02-24 07:52:06.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:06.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:06.727][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-02-24 07:52:09.124][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-02-24 07:52:10.288][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:10.314][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-02-24 07:52:10.329][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-02-24 07:52:10.343][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-02-24 07:52:10.348][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:10.370][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:10.372][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:10.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:10.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:10.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:10.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:10.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:10.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:10.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:10.399][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.401][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.404][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.417][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:10.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:10.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.422][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.424][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:10.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:10.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.429][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.431][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:10.432][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:10.434][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.435][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.437][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:10.439][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:10.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.442][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.444][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:10.445][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:10.447][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.448][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.450][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:10.452][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.455][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:10.458][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:10.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.461][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.463][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:10.464][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:10.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.467][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:10.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:10.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.480][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:10.482][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:10.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.485][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.487][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:10.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:10.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.497][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:10.498][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:10.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.501][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:10.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:10.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:10.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:10.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:10.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:10.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:10.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:10.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:10.586][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-02-24 07:52:10.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:10.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:10.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:10.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:10.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:10.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:10.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:10.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:10.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:10.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:10.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:10.639][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-02-24 07:52:10.640][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:10.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-02-24 07:52:10.645][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:10.647][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:10.649][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:10.650][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:10.652][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:10.654][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:10.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:10.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:10.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:10.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:10.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:10.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:10.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:10.676][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-02-24 07:52:10.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:10.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:10.683][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-02-24 07:52:11.850][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-02-24 07:52:13.191][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:13.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-02-24 07:52:13.215][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-02-24 07:52:13.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-02-24 07:52:13.234][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:13.271][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:13.272][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:13.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:13.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:13.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:13.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:13.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:13.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:13.289][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[2023-02-24 07:52:13.292][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.294][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.295][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.296][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.307][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:13.309][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:13.310][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.312][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.314][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:13.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.323][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:13.325][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:13.327][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.328][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:13.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:13.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.340][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:13.341][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:13.343][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.344][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:13.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:13.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.355][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:13.357][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:13.358][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.360][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:13.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:13.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.371][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:13.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:13.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.375][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.377][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:13.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:13.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.387][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:13.388][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.390][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.391][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.393][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:13.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.402][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:13.404][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:13.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.406][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:13.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:13.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.418][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:13.419][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:13.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.422][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.424][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:13.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:13.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.434][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:13.436][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:13.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.438][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.440][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.450][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:13.451][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:13.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.454][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.456][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:13.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:13.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:13.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:13.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:13.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:13.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:13.564][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-02-24 07:52:13.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:13.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:13.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:13.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:13.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:13.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:13.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:13.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:13.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:13.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:13.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:13.597][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-02-24 07:52:13.599][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:13.601][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-02-24 07:52:13.603][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:13.604][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:13.606][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:13.607][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:13.608][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:13.610][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:13.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:13.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:13.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:13.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:13.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:13.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:13.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:13.629][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-02-24 07:52:13.633][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:13.635][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:13.637][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-02-24 07:52:14.778][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-02-24 07:52:16.943][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:16.952][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-02-24 07:52:16.967][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-02-24 07:52:16.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-02-24 07:52:16.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:17.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:17.022][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:17.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:17.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:17.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:17.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:17.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:17.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:17.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:17.044][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.045][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.048][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.059][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:17.060][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:17.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.063][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:17.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:17.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.074][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:17.075][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:17.077][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.078][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.080][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:17.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:17.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:17.091][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:17.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.093][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:17.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:17.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:17.106][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:17.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.108][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:17.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:17.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.119][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:17.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:17.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.124][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.125][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:17.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:17.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.135][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:17.136][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.139][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.140][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:17.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:17.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:17.153][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.154][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:17.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:17.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.165][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:17.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:17.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.169][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:17.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:17.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.180][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:17.182][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:17.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.184][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:17.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:17.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:17.197][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:17.199][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.200][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:17.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:17.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:17.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:17.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:17.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:17.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:17.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:17.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:17.280][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-02-24 07:52:17.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:17.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:17.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:17.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:17.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:17.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:17.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:17.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:17.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:17.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:17.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:17.313][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-02-24 07:52:17.315][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:17.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-02-24 07:52:17.318][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:17.320][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:17.321][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:17.323][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:17.324][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:17.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:17.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:17.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:17.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:17.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:17.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:17.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:17.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:17.346][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-02-24 07:52:17.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:17.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:17.353][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-02-24 07:52:18.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-02-24 07:52:20.698][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:20.709][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-02-24 07:52:20.727][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-02-24 07:52:20.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-02-24 07:52:20.749][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:20.791][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:20.801][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:20.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:20.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:20.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:20.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:20.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:20.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:20.821][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.TRACE[2023-02-24 07:52:20.824][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:20.826][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:20.828][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.829][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:20.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:20.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.842][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:20.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:20.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.847][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:20.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.860][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:20.862][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:20.864][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.866][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.868][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:20.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:20.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.879][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:20.880][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:20.882][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.883][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:20.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:20.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:20.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.899][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.911][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:20.912][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:20.914][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.915][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.917][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:20.918][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:20.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.921][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.923][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:20.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:20.934][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:20.936][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.937][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:20.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:20.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.948][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:20.950][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:20.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.953][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:20.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:20.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.964][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:20.965][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:20.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.968][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:20.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:20.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.979][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:20.981][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:20.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.983][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:20.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:20.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:20.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:20.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:20.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:20.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:21.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:21.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:21.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:21.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:21.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:21.086][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-02-24 07:52:21.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:21.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:21.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:21.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:21.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:21.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:21.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:21.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:21.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:21.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:21.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:21.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:21.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:21.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:21.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:21.128][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-02-24 07:52:21.129][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:21.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-02-24 07:52:21.134][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:21.136][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:21.137][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:21.139][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:21.140][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:21.142][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:21.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:21.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:21.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:21.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:21.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:21.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:21.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:21.164][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-02-24 07:52:21.169][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:21.170][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:21.172][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-02-24 07:52:23.622][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-02-24 07:52:25.020][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:25.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-02-24 07:52:25.047][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-02-24 07:52:25.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-02-24 07:52:25.067][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:25.091][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:25.093][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:25.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:25.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:25.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:25.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:25.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:25.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:25.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:25.128][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.132][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.143][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:25.144][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:25.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.147][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.149][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:25.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:25.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.158][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:25.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:25.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.162][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:25.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.173][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:25.175][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:25.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.178][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.189][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:25.191][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:25.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.193][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:25.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:25.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.204][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:25.205][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:25.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.208][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.210][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:25.211][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.214][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.216][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:25.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.225][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:25.226][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:25.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.229][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:25.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:25.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.240][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:25.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:25.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.244][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:25.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:25.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.255][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:25.257][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:25.258][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.259][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.261][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:25.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.270][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:25.271][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:25.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.274][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:25.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:25.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:25.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:25.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:25.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:25.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:25.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:25.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:25.351][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-02-24 07:52:25.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:25.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:25.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:25.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:25.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:25.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:25.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:25.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:25.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:25.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:25.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:25.385][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-02-24 07:52:25.387][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:25.389][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-02-24 07:52:25.391][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:25.392][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:25.394][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:25.395][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:25.396][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:25.398][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:25.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:25.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:25.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:25.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:25.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:25.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:25.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:25.417][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-02-24 07:52:25.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:25.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:25.424][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-02-24 07:52:26.533][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-02-24 07:52:27.650][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:27.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-02-24 07:52:27.674][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-02-24 07:52:27.688][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-02-24 07:52:27.693][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:27.717][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:27.719][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:27.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:27.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:27.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:27.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:27.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:27.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:27.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:27.739][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:27.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:27.758][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.759][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:27.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:27.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.770][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:27.772][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:27.773][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.781][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.789][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:27.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:27.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.810][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:27.812][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:27.813][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.815][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.817][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:27.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:27.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.827][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:27.828][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:27.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.831][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:27.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:27.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.844][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:27.846][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:27.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.849][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:27.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:27.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.861][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:27.863][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:27.864][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.866][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.868][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:27.870][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:27.871][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.873][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.875][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:27.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:27.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.886][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:27.887][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:27.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.890][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:27.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:27.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.903][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:27.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:27.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.908][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:27.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:27.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.921][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:27.923][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:27.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.927][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.929][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:27.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:27.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.940][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:27.942][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:27.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.945][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:27.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:27.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:27.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:27.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:27.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:27.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:27.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:27.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:27.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:27.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:27.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:27.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:27.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:27.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:27.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:27.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:28.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:28.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:28.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:28.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:28.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:28.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:28.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:28.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:28.025][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-02-24 07:52:28.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:28.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:28.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:28.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:28.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:28.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:28.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:28.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:28.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:28.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:28.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:28.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:28.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:28.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:28.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:28.079][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-02-24 07:52:28.081][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:28.083][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-02-24 07:52:28.085][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:28.087][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:28.088][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:28.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:28.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:28.093][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:28.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:28.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:28.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:28.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:28.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:28.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:28.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:28.114][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-02-24 07:52:28.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:28.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:28.121][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-02-24 07:52:29.240][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-02-24 07:52:30.360][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:30.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-02-24 07:52:30.384][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-02-24 07:52:30.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-02-24 07:52:30.403][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:30.426][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:30.428][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:30.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:30.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:30.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:30.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:30.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:30.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:30.444][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[2023-02-24 07:52:30.447][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.450][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.452][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.477][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:30.479][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:30.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.482][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.483][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:30.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:30.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.493][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:30.494][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:30.496][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.497][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:30.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.508][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:30.510][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:30.511][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.512][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:30.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:30.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.523][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:30.525][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:30.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.528][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:30.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:30.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.539][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:30.540][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:30.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.543][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.545][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:30.546][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.549][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.551][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:30.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.560][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:30.562][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:30.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.565][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:30.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.576][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:30.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:30.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.580][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:30.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:30.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.591][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:30.593][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:30.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.596][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.598][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:30.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:30.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.607][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:30.609][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:30.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.612][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:30.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:30.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:30.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:30.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:30.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:30.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:30.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:30.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:30.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:30.684][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-02-24 07:52:30.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:30.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:30.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:30.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:30.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:30.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:30.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:30.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:30.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:30.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:30.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:30.727][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-02-24 07:52:30.729][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:30.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-02-24 07:52:30.733][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:30.734][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:30.736][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:30.737][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:30.739][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:30.740][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:30.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:30.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:30.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:30.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:30.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:30.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:30.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:30.760][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-02-24 07:52:30.764][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:30.765][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:30.767][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-02-24 07:52:31.870][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-02-24 07:52:34.587][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:34.600][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-02-24 07:52:34.619][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-02-24 07:52:34.634][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-02-24 07:52:34.640][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:34.666][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:34.668][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:34.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:34.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:34.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:34.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:34.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:34.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:34.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:34.691][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.696][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.708][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:34.710][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:34.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.733][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:34.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:34.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.747][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:34.748][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:34.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.751][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:34.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:34.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.764][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:34.765][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:34.767][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.769][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:34.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:34.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:34.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:34.784][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.785][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:34.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.798][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:34.800][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:34.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.803][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.805][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:34.806][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.809][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.812][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:34.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:34.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:34.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.827][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:34.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.840][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:34.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:34.843][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.844][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:34.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:34.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.857][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:34.858][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:34.860][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.861][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:34.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:34.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.873][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:34.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:34.876][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.877][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.879][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:34.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:34.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:34.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:34.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:34.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:34.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:34.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:34.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:34.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:34.951][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-02-24 07:52:34.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:34.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:34.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:34.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:34.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:34.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:34.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:34.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:34.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:34.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:34.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:34.995][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-02-24 07:52:34.996][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:34.999][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-02-24 07:52:35.000][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:35.002][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:35.004][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:35.005][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:35.006][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:35.008][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:35.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:35.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:35.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:35.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:35.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:35.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:35.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:35.028][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-02-24 07:52:35.032][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:35.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:35.036][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-02-24 07:52:36.160][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-02-24 07:52:37.349][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:37.360][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-02-24 07:52:37.377][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-02-24 07:52:37.392][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-02-24 07:52:37.398][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:37.422][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:37.424][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:37.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:37.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:37.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:37.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:37.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:37.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:37.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:37.446][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.447][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.450][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.462][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:37.464][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:37.465][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.467][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:37.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.496][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:37.498][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:37.499][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.500][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:37.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:37.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.512][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:37.514][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:37.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.517][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.518][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:37.520][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:37.521][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.523][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.525][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:37.526][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:37.527][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.529][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.531][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:37.532][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.533][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.535][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.537][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.546][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:37.548][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:37.549][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.551][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:37.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:37.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.563][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:37.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:37.566][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.567][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:37.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:37.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.579][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:37.581][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:37.582][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.584][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:37.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.595][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:37.597][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:37.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.600][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:37.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:37.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:37.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:37.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:37.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:37.671][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-02-24 07:52:37.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:37.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:37.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:37.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:37.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:37.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:37.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:37.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:37.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:37.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:37.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:37.709][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-02-24 07:52:37.710][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:37.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-02-24 07:52:37.715][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:37.716][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:37.718][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:37.719][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:37.721][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:37.722][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:37.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:37.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:37.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:37.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:37.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:37.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:37.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:37.762][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-02-24 07:52:37.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:37.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:37.769][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-02-24 07:52:38.894][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-02-24 07:52:40.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:40.060][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-02-24 07:52:40.079][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-02-24 07:52:40.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-02-24 07:52:40.105][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:40.131][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:40.134][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:40.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:40.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:40.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:40.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:40.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:40.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:40.152][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.TRACE[2023-02-24 07:52:40.156][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.157][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.161][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.172][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:40.174][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:40.175][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.177][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.179][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:40.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.188][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:40.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:40.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.193][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:40.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:40.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.206][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:40.207][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:40.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.210][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.212][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:40.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:40.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.216][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.218][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:40.220][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:40.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.238][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.240][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:40.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.243][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.244][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.246][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:40.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.255][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:40.257][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:40.258][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.259][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:40.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:40.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.270][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:40.272][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:40.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.275][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:40.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:40.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.286][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:40.288][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:40.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.291][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.292][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:40.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:40.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.302][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:40.304][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:40.305][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.307][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:40.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:40.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:40.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:40.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:40.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:40.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:40.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:40.374][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-02-24 07:52:40.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:40.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:40.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:40.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:40.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:40.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:40.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:40.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:40.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:40.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:40.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:40.410][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-02-24 07:52:40.411][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:40.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-02-24 07:52:40.415][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:40.417][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:40.418][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:40.420][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:40.421][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:40.423][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:40.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:40.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:40.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:40.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:40.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:40.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:40.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:40.443][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-02-24 07:52:40.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:40.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:40.450][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-02-24 07:52:41.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-02-24 07:52:42.754][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:42.764][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-02-24 07:52:42.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-02-24 07:52:42.795][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-02-24 07:52:42.800][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:42.823][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:42.825][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:42.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:42.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:42.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:42.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:42.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:42.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:42.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:42.844][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:42.846][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:42.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.848][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:42.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:42.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.859][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:42.861][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:42.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.863][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.865][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.874][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:42.876][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:42.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.878][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:42.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:42.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.899][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:42.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:42.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.905][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:42.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.922][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:42.924][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:42.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.927][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:42.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:42.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:42.942][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:42.944][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.945][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.948][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:42.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:42.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.953][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:42.955][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:42.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:42.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:42.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.015][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:43.017][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:43.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.020][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:43.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.032][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:43.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:43.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.036][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:43.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:43.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.048][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:43.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:43.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.053][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.055][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:43.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.065][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:43.067][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:43.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.070][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.072][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:43.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:43.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:43.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:43.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:43.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:43.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:43.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:43.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:43.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:43.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:43.147][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-02-24 07:52:43.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:43.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:43.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:43.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:43.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:43.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:43.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:43.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:43.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:43.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:43.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:43.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:43.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:43.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:43.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:43.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:43.183][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-02-24 07:52:43.185][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:43.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-02-24 07:52:43.189][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:43.190][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:43.192][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:43.193][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:43.195][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:43.196][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:43.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:43.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:43.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:43.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:43.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:43.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:43.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:43.217][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-02-24 07:52:43.221][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:43.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:43.225][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-02-24 07:52:45.790][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-02-24 07:52:46.915][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:46.925][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-02-24 07:52:46.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-02-24 07:52:46.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-02-24 07:52:46.959][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:46.982][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:46.983][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:46.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:46.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:46.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:46.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:46.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:46.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:47.000][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.TRACE[2023-02-24 07:52:47.003][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.005][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.007][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.018][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:47.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:47.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.022][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.027][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:47.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:47.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.036][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:47.038][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:47.039][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.040][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:47.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:47.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.051][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:47.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:47.054][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.055][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:47.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:47.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.067][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:47.068][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:47.070][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.071][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:47.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:47.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:47.084][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:47.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.086][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.088][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:47.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.091][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.092][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:47.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.111][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:47.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:47.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.120][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:47.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:47.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.131][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:47.132][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:47.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.135][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:47.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:47.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.146][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:47.148][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:47.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.151][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.152][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:47.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:47.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.162][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:47.163][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:47.165][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.166][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:47.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:47.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:47.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:47.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:47.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:47.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:47.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:47.239][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-02-24 07:52:47.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:47.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:47.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:47.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:47.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:47.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:47.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:47.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:47.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:47.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:47.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:47.273][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-02-24 07:52:47.274][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:47.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-02-24 07:52:47.278][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:47.280][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:47.281][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:47.283][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:47.284][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:47.285][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:47.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:47.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:47.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:47.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:47.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:47.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:47.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:47.305][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-02-24 07:52:47.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:47.311][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:47.313][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-02-24 07:52:49.447][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-02-24 07:52:50.633][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:50.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-02-24 07:52:50.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-02-24 07:52:50.680][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-02-24 07:52:50.686][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:50.717][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:50.719][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:50.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:50.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:50.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:50.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:50.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:50.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:50.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:50.745][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.746][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.748][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.749][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.761][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:50.763][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:50.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.766][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:50.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:50.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.779][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:50.781][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:50.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.784][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:50.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:50.797][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:50.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.800][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:50.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:50.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.812][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:50.813][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:50.815][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.816][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:50.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:50.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.828][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:50.830][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:50.831][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.833][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.835][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:50.836][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:50.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.839][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.841][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:50.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:50.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:50.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:50.869][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.875][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:50.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:50.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.887][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:50.889][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:50.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.891][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:50.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:50.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.903][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:50.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:50.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.907][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.909][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:50.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:50.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.918][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:50.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:50.921][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.923][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.924][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:50.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:50.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:50.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:50.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:50.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:50.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:50.995][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-02-24 07:52:50.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:50.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:51.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:51.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:51.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:51.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:51.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:51.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:51.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:51.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:51.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:51.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:51.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:51.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:51.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:51.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:51.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:51.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:51.030][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-02-24 07:52:51.031][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:51.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-02-24 07:52:51.035][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:51.037][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:51.038][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:51.040][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:51.041][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:51.042][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:51.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:51.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:51.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:51.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:51.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:51.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:51.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:51.063][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-02-24 07:52:51.066][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:51.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:51.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-02-24 07:52:52.197][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-02-24 07:52:53.334][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:53.344][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-02-24 07:52:53.360][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-02-24 07:52:53.375][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-02-24 07:52:53.381][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:53.403][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:53.405][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:53.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:53.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:53.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:53.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:53.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:53.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:53.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:53.425][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.427][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.429][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.440][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:53.442][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:53.443][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.445][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.447][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:53.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.456][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:53.458][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:53.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.460][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:53.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.471][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:53.473][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:53.474][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.476][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.487][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:53.488][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:53.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.491][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:53.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:53.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.502][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:53.503][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:53.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.506][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.508][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:53.509][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.512][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:53.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.523][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:53.525][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:53.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.527][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:53.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:53.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.551][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:53.553][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:53.554][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.556][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:53.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.567][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:53.569][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:53.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.572][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.573][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:53.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:53.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.583][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:53.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:53.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.587][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:53.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:53.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:53.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:53.678][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-02-24 07:52:53.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:53.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:53.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:53.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:53.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:53.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:53.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:53.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:53.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:53.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:53.723][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-02-24 07:52:53.725][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:52:53.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-02-24 07:52:53.730][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:52:53.732][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:52:53.734][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:52:53.736][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:52:53.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:52:53.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:52:53.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:53.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:53.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:53.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:53.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:53.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:53.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:52:53.764][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-02-24 07:52:53.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:53.772][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:53.775][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-02-24 07:52:55.582][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-02-24 07:52:56.770][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:52:56.783][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-02-24 07:52:56.803][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-02-24 07:52:56.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-02-24 07:52:56.826][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:52:56.852][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:52:56.854][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:52:56.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:56.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:56.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:56.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:56.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:56.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:56.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:56.875][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:56.877][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:56.878][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.880][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:56.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:56.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.891][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:56.892][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:56.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.895][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.897][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:52:56.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:52:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.906][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:56.908][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:56.909][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.910][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.912][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:52:56.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:52:56.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.922][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:56.923][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:56.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.926][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:52:56.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:52:56.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.937][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:56.939][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:56.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.941][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:52:56.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:52:56.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.953][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:56.954][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:52:56.956][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.957][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.959][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:56.960][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:56.962][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.963][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.965][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:52:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:56.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:56.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:56.977][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.978][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:56.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:56.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:56.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:56.989][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:56.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:56.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.002][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:52:57.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:52:57.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.018][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:57.020][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:57.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.022][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.024][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:52:57.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:52:57.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.033][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:57.035][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:57.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.038][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.039][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:52:57.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:52:57.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:57.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:57.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:57.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:57.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:52:57.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:52:57.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:52:57.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:52:57.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.110][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-02-24 07:52:57.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.177][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:52:57.181][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:52:57.183][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-24 07:52:57.185][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:52:57.187][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-24 07:52:57.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:57.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:52:57.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:52:57.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:52:57.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:52:57.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:52:57.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:52:57.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:52:57.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:52:57.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:57.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:57.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:57.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:52:58.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:58.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:52:58.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:52:58.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:52:58.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:52:58.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:52:58.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:52:58.101][private$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[2023-02-24 07:52:59.256][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[2023-02-24 07:53:00.380][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:00.390][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-02-24 07:53:00.406][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-02-24 07:53:00.415][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[2023-02-24 07:53:00.419][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:00.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:00.423][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:53:01.690][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:53:02.881][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:02.894][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-02-24 07:53:02.915][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-02-24 07:53:02.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:02.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:02.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:02.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:02.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:02.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:02.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:02.946][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-02-24 07:53:02.948][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:53:02.950][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-02-24 07:53:02.952][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:53:02.954][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:53:02.956][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:53:02.958][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:02.959][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:53:02.961][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:53:02.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:02.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:02.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:02.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:02.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:02.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:02.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:02.984][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-02-24 07:53:02.988][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:02.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:02.992][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-02-24 07:53:04.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-02-24 07:53:06.558][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:06.568][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-02-24 07:53:06.584][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-02-24 07:53:06.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-02-24 07:53:06.605][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:53:06.648][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:53:06.650][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:53:06.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:06.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:06.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:06.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:06.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:06.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:06.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:06.670][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.671][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.674][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.685][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:06.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:06.688][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.689][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:06.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:06.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.700][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:06.702][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:06.703][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.705][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.707][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:06.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:06.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.716][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:06.717][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:06.719][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.720][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:06.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:06.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.731][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:06.733][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:06.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.736][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:06.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:06.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.746][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:06.748][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:06.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.750][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:06.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:06.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.761][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:06.763][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:06.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.765][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.767][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.776][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.777][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.779][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.780][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.791][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:06.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:06.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.795][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:06.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:06.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.807][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:06.808][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:06.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.811][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.813][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:06.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:06.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.822][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:06.823][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:06.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.826][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:06.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:06.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:06.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:06.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:06.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:06.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:06.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:06.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:06.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:06.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:06.905][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-02-24 07:53:06.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:06.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:06.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:06.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:06.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:06.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:06.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:06.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:06.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:06.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:06.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:06.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:06.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:06.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:06.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:06.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:06.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:06.971][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-02-24 07:53:06.972][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:53:06.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-02-24 07:53:06.976][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:53:06.978][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:53:06.979][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:53:06.981][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:06.982][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:53:06.984][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:53:06.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:06.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:06.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:06.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:07.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:07.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:07.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:07.005][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-02-24 07:53:07.009][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:07.010][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:07.012][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-02-24 07:53:08.138][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-02-24 07:53:09.541][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:09.611][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-02-24 07:53:09.633][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-02-24 07:53:09.651][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-02-24 07:53:09.658][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:53:09.683][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:53:09.685][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:53:09.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:09.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:09.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:09.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:09.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:09.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:09.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:09.707][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.711][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.723][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:09.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:09.726][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.727][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.729][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:09.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:09.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.739][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:09.741][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:09.742][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.744][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:09.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:09.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.755][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:09.757][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:09.758][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.760][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:09.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:09.773][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:09.774][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.776][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:09.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:09.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.788][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:09.789][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:09.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.792][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.794][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:09.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:09.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.798][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:09.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:09.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.809][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.811][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.814][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.825][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:09.827][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:09.828][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.829][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:09.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:09.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.841][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:09.842][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:09.843][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.845][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:09.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:09.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.865][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:09.867][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:09.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.870][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.871][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:09.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:09.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:09.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:09.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:09.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:09.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:09.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:09.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:09.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:09.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:09.940][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-02-24 07:53:09.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:09.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:09.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:09.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.013][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:10.018][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:10.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-24 07:53:10.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:10.023][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-24 07:53:10.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.733][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:10.738][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:10.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-02-24 07:53:10.741][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:10.743][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-02-24 07:53:10.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:10.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:10.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:10.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:10.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:10.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:10.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:10.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:10.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:10.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:10.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:10.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:11.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.445][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:11.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:11.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-24 07:53:11.467][biodb::testThat]
biodb.INFO [2023-02-24 07:53:11.469][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-02-24 07:53:11.474][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:11.483][biodb::testThat]
biodb.TRACE[2023-02-24 07:53:11.495][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-24 07:53:11.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-24 07:53:11.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:11.641][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:11.648][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:11.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-02-24 07:53:11.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:11.656][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-02-24 07:53:11.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.703][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:11.708][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:11.710][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-02-24 07:53:11.712][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:11.714][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-02-24 07:53:11.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:11.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:11.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:11.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:11.969][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:11.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-02-24 07:53:11.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:11.974][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-02-24 07:53:11.977][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-24 07:53:11.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:11.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:11.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:11.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:11.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:11.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:11.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:11.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:11.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:11.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:11.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.006][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.007][private$selectFields]
biodb.TRACE[2023-02-24 07:53:12.008][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:12.010][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:12.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.017][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.022][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.023][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.025][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.026][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.029][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.030][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.031][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:12.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.062][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-02-24 07:53:12.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:12.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:12.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:12.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:12.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:12.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:12.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:12.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.092][private$selectFields]
biodb.TRACE[2023-02-24 07:53:12.093][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:12.094][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:12.096][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.100][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.101][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.102][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.106][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.108][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.109][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:12.111][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.112][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.115][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.116][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:12.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:12.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.135][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-24 07:53:12.137][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-24 07:53:12.138][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-24 07:53:12.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:12.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:12.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:12.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:12.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:12.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:12.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:12.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:12.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:12.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:12.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:12.333][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[2023-02-24 07:53:12.338][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:12.340][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:12.342][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:53:13.476][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:53:14.615][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:14.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-02-24 07:53:14.639][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-02-24 07:53:14.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:14.652][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:14.653][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:14.656][private$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[2023-02-24 07:53:15.763][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[2023-02-24 07:53:16.870][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:16.880][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-02-24 07:53:16.896][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-02-24 07:53:16.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:16.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:16.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:16.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:16.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:16.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:16.918][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.TRACE[2023-02-24 07:53:16.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:16.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:16.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:16.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:16.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:16.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:16.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:16.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:16.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:16.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:16.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:16.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:16.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:16.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:16.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:16.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:16.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:16.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:16.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:16.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:16.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:16.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:16.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:16.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.035][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-24 07:53:17.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.084][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.TRACE[2023-02-24 07:53:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.096][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.097][private$selectFields]
biodb.TRACE[2023-02-24 07:53:17.099][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:17.100][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:17.101][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.106][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.108][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.109][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.112][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.113][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.114][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.116][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.117][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.140][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.142][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:17.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.160][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-02-24 07:53:17.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.233][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.234][private$selectFields]
biodb.TRACE[2023-02-24 07:53:17.236][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:17.237][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:17.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.240][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.241][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.244][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.245][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.249][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.250][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.265][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.268][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.270][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.272][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:17.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.289][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-24 07:53:17.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.317][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.318][private$selectFields]
biodb.TRACE[2023-02-24 07:53:17.319][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:17.320][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:17.322][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.323][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.327][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.328][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.330][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.331][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.332][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.335][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.336][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.338][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.340][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.341][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:17.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.359][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-02-24 07:53:17.360][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-24 07:53:17.362][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-24 07:53:17.373][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:17.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:17.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-24 07:53:17.379][biodb::testThat]
biodb.INFO [2023-02-24 07:53:17.381][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-02-24 07:53:17.382][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:17.383][biodb::testThat]
biodb.TRACE[2023-02-24 07:53:17.388][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-24 07:53:17.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-24 07:53:17.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.438][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[2023-02-24 07:53:17.494][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[2023-02-24 07:53:17.499][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:17.501][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-02-24 07:53:17.502][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:17.504][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-02-24 07:53:17.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.549][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[2023-02-24 07:53:17.554][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:17.556][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-02-24 07:53:17.557][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:17.559][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-02-24 07:53:17.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:17.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.594][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[2023-02-24 07:53:17.599][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:17.600][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-02-24 07:53:17.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:17.604][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-02-24 07:53:17.607][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-24 07:53:17.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.643][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.644][private$selectFields]
biodb.TRACE[2023-02-24 07:53:17.646][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:17.647][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:17.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.654][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.656][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.657][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.660][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.661][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.663][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.667][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.669][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.670][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:17.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.690][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-02-24 07:53:17.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.723][private$selectFields]
biodb.TRACE[2023-02-24 07:53:17.725][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:17.726][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:17.728][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.731][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.732][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.733][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.735][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.736][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.738][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.739][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.741][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.742][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:17.744][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.745][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.747][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.748][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.750][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:17.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.769][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-24 07:53:17.771][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-24 07:53:17.772][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-24 07:53:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:17.895][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:17.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:17.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-02-24 07:53:17.903][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:17.905][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-02-24 07:53:17.910][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:17.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:17.916][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-02-24 07:53:17.918][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:17.920][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-02-24 07:53:17.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:17.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:17.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:17.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:17.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:17.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:17.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:17.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:17.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:17.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.042][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-24 07:53:18.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.073][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.074][private$selectFields]
biodb.TRACE[2023-02-24 07:53:18.076][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:18.077][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:18.079][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.081][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.084][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.090][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.091][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.093][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.098][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.100][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:18.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.118][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-02-24 07:53:18.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.134][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.TRACE[2023-02-24 07:53:18.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.146][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.147][private$selectFields]
biodb.TRACE[2023-02-24 07:53:18.148][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:18.150][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:18.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.154][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.155][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.157][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.158][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.159][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.162][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.163][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.165][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.170][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.171][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:18.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.190][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-24 07:53:18.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.218][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.219][private$selectFields]
biodb.TRACE[2023-02-24 07:53:18.221][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:18.222][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:18.223][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.229][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.231][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.233][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.234][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.235][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.237][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.242][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.243][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.261][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-02-24 07:53:18.263][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-24 07:53:18.264][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-24 07:53:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:18.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:18.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-24 07:53:18.282][biodb::testThat]
biodb.INFO [2023-02-24 07:53:18.284][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-02-24 07:53:18.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:18.286][biodb::testThat]
biodb.TRACE[2023-02-24 07:53:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-24 07:53:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-24 07:53:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:18.396][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:18.401][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:18.403][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-02-24 07:53:18.404][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:18.406][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-02-24 07:53:18.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.451][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:18.455][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:18.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-02-24 07:53:18.459][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:18.461][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-02-24 07:53:18.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:18.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.497][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:18.501][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:18.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-02-24 07:53:18.505][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:18.507][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-02-24 07:53:18.510][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-24 07:53:18.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.538][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.540][private$selectFields]
biodb.TRACE[2023-02-24 07:53:18.541][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:18.542][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:18.544][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.545][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.547][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.549][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.551][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.552][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.555][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.558][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.559][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.560][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.563][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.564][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:18.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.583][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-02-24 07:53:18.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.611][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.612][private$selectFields]
biodb.TRACE[2023-02-24 07:53:18.614][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:18.615][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:18.616][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.622][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.623][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.627][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.629][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.630][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.632][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.633][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.634][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.636][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.637][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:18.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.656][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-24 07:53:18.657][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-24 07:53:18.659][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-24 07:53:18.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.735][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[2023-02-24 07:53:18.788][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[2023-02-24 07:53:18.792][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:18.794][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-02-24 07:53:18.796][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:18.797][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-02-24 07:53:18.801][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[2023-02-24 07:53:18.806][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:18.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-02-24 07:53:18.809][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:18.811][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-02-24 07:53:18.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:18.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:18.919][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-24 07:53:18.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:18.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:18.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:18.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:18.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:18.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.947][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.949][private$selectFields]
biodb.TRACE[2023-02-24 07:53:18.950][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:18.951][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:18.952][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.954][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.955][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.958][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.961][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.962][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.963][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.965][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.966][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:18.967][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.971][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.973][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:18.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:18.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:18.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:18.991][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-02-24 07:53:18.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:18.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:18.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:19.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:19.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:19.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:19.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:19.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.020][private$selectFields]
biodb.TRACE[2023-02-24 07:53:19.021][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:19.022][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:19.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.029][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.030][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.032][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.033][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.034][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.036][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.037][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.038][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.040][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.042][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.044][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:19.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.062][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-02-24 07:53:19.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:19.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:19.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:19.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:19.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:19.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:19.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:19.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.091][private$selectFields]
biodb.TRACE[2023-02-24 07:53:19.092][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-24 07:53:19.094][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-24 07:53:19.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.100][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.102][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.105][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.107][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.108][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-02-24 07:53:19.109][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.113][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.115][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-02-24 07:53:19.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:19.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:19.132][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-02-24 07:53:19.134][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-24 07:53:19.135][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-24 07:53:19.164][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:19.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-24 07:53:19.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:19.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-24 07:53:19.171][biodb::testThat]
biodb.INFO [2023-02-24 07:53:19.172][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-02-24 07:53:19.173][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:19.175][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:19.177][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-02-24 07:53:19.179][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:53:19.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-02-24 07:53:19.183][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:53:19.184][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:53:19.185][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:53:19.187][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:19.188][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:53:19.190][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:53:19.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:19.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:19.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:19.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:19.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:19.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:19.207][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[2023-02-24 07:53:19.209][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-02-24 07:53:19.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:19.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:19.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-02-24 07:53:20.301][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-02-24 07:53:21.453][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:21.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-02-24 07:53:21.493][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-02-24 07:53:21.507][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-02-24 07:53:21.512][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:53:21.533][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:53:21.535][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:53:21.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:21.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:21.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:21.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:21.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:21.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:21.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:21.555][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.559][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.569][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:21.571][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:21.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.573][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.575][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:21.576][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:21.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.579][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.581][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:21.582][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:21.583][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.585][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.586][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:21.588][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:21.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.590][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.592][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:21.593][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:21.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.596][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.597][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:21.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:21.600][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.601][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:21.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:21.605][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.606][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.608][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:21.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:21.611][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.612][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.614][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:21.615][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:21.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.618][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.620][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:21.621][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:21.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.624][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:21.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:21.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:21.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:21.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:21.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:21.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:21.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:21.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:21.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:21.683][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-02-24 07:53:21.685][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-02-24 07:53:21.694][biodb::testThat]
biodb.INFO [2023-02-24 07:53:21.696][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-02-24 07:53:21.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:21.698][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:21.712][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-02-24 07:53:21.714][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-02-24 07:53:21.715][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-02-24 07:53:21.717][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-02-24 07:53:21.719][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-02-24 07:53:21.721][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:53:21.722][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:53:21.723][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:21.725][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:53:21.726][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:53:21.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:21.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:21.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:21.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:21.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:21.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:21.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:21.748][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-02-24 07:53:21.752][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:21.753][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:21.755][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-02-24 07:53:22.924][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-02-24 07:53:24.080][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:24.093][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-02-24 07:53:24.111][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-02-24 07:53:24.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:24.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:24.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:24.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:24.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:24.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:24.138][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[2023-02-24 07:53:24.140][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-02-24 07:53:24.144][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:24.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:24.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-02-24 07:53:25.312][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-02-24 07:53:26.731][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:26.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-02-24 07:53:26.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-02-24 07:53:26.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:26.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:26.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:26.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:26.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:26.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:26.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:26.789][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-02-24 07:53:26.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:26.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:26.798][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-02-24 07:53:28.655][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-02-24 07:53:31.052][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:31.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-02-24 07:53:31.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-02-24 07:53:31.096][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-02-24 07:53:31.103][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:53:31.130][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-02-24 07:53:31.132][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-02-24 07:53:31.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:31.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:31.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:31.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:31.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:31.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:31.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:31.159][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.160][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.162][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.163][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.176][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:31.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:31.179][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.181][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.183][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:31.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:31.186][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.187][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.189][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:31.191][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:31.193][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.194][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.196][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.197][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.199][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.200][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.205][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.207][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.209][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:31.210][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:31.212][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.213][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.215][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.216][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.219][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.221][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:31.223][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:31.224][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.225][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.228][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:31.229][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:31.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.232][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.234][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:31.235][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:31.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.238][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:31.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:31.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:31.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:31.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:31.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:31.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:31.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:53:31.299][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.301][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.302][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.303][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.314][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:31.316][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:31.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.318][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.320][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:31.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:31.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.329][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:31.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:31.332][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.333][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:31.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:31.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.344][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:31.346][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:31.347][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.348][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:31.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:31.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.360][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.362][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.363][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.364][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.393][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.395][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.397][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.399][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.408][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:31.409][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:31.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.412][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.414][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:31.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:31.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.423][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.427][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.438][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:31.439][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:31.441][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.442][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.453][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:31.454][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:31.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.457][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.459][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:31.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:31.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.468][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:31.470][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:31.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.472][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.474][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:31.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:31.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:31.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:31.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:31.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:31.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:31.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:31.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:31.538][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[2023-02-24 07:53:31.541][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.542][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.544][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.545][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.556][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:31.564][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:31.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.575][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.580][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:53:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:53:31.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.603][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:31.605][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:31.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.610][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:53:31.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:53:31.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.626][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:31.628][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:31.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.631][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:53:31.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:53:31.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.645][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.649][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.651][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:53:31.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.666][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.668][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.672][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:53:31.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.687][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:31.689][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:31.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.693][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:53:31.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:53:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.708][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.710][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.712][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.714][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:31.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.729][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:31.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:31.732][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.734][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:31.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:31.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.749][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:31.751][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:31.753][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.755][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:53:31.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:53:31.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.771][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:31.773][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:31.775][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.776][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:53:31.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:53:31.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:53:31.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:31.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:53:31.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:53:31.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:31.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:53:31.902][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-02-24 07:53:31.903][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-02-24 07:53:31.905][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-02-24 07:53:31.938][biodb::testThat]
biodb.INFO [2023-02-24 07:53:31.939][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-02-24 07:53:31.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:31.942][biodb::testThat]
biodb.INFO [2023-02-24 07:53:31.982][biodb::testThat]
biodb.INFO [2023-02-24 07:53:31.984][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-02-24 07:53:31.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:31.987][biodb::testThat]
biodb.INFO [2023-02-24 07:53:31.998][biodb::testThat]
biodb.INFO [2023-02-24 07:53:32.000][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-02-24 07:53:32.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:32.003][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:32.008][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[2023-02-24 07:53:32.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:32.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:32.019][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:53:33.317][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:53:36.061][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:36.075][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-02-24 07:53:36.095][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-02-24 07:53:36.123][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:53:36.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:53:36.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:36.127][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:53:36.128][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:36.130][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:53:36.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:53:36.133][ef$get] fields variable is a list.
biodb.INFO [2023-02-24 07:53:36.135][biodb::testThat]
biodb.INFO [2023-02-24 07:53:36.136][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-02-24 07:53:36.137][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:36.138][biodb::testThat]
biodb.ERROR[2023-02-24 07:53:36.158][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-02-24 07:53:36.178][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-02-24 07:53:36.191][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-24 07:53:36.193][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-24 07:53:36.195][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-24 07:53:36.196][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-24 07:53:36.197][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.200][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.202][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-24 07:53:36.220][biodb::testContext]
biodb.INFO [2023-02-24 07:53:36.222][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:53:36.223][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-02-24 07:53:36.224][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:53:36.225][biodb::testContext]
biodb.INFO [2023-02-24 07:53:36.232][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:53:36.234][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-24 07:53:36.239][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:36.241][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-24 07:53:36.243][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-24 07:53:36.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.246][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[2023-02-24 07:53:36.248][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-24 07:53:36.249][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-24 07:53:36.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.254][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-24 07:53:36.255][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-24 07:53:36.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.259][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[2023-02-24 07:53:36.260][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-24 07:53:36.262][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-24 07:53:36.263][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-24 07:53:36.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.268][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-24 07:53:36.269][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-24 07:53:36.271][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-24 07:53:36.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.276][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-24 07:53:36.277][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-24 07:53:36.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.282][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-24 07:53:36.283][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-24 07:53:36.285][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-24 07:53:36.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.289][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.DEBUG[2023-02-24 07:53:36.290][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-24 07:53:36.291][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-24 07:53:36.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.296][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-24 07:53:36.298][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-24 07:53:36.299][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-24 07:53:36.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.304][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:53:36.306][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-24 07:53:36.307][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-24 07:53:36.308][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-24 07:53:36.310][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-24 07:53:36.311][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-24 07:53:36.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.316][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-24 07:53:36.318][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-24 07:53:36.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.323][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-24 07:53:36.324][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-24 07:53:36.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.329][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-24 07:53:36.331][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-24 07:53:36.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.336][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-24 07:53:36.337][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-24 07:53:36.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.342][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-24 07:53:36.344][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-24 07:53:36.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.349][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:53:36.351][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-24 07:53:36.355][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-24 07:53:36.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.375][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-24 07:53:36.377][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-24 07:53:36.379][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-24 07:53:36.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.384][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-24 07:53:36.387][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.389][self$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[2023-02-24 07:53:36.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:36.393][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.394][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.396][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.397][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.398][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:53:36.400][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:36.401][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.402][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-24 07:53:36.404][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:36.405][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.407][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.408][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:36.408][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:36.408][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:36.408][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:53:36.408][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:53:36.409][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:36.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.413][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:36.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.417][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.419][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.420][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:36.421][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:36.423][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.424][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.426][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-24 07:53:36.429][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.430][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:53:36.431][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:36.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.437][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.438][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.440][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:53:36.441][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:36.442][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.444][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-24 07:53:36.445][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:36.446][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.448][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.449][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:36.449][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:36.449][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:36.449][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:53:36.449][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:53:36.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:36.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.454][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:36.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.458][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.459][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:36.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:36.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.465][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.466][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-24 07:53:36.469][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.470][self$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[2023-02-24 07:53:36.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:36.474][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.477][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.480][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:53:36.481][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:36.482][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.484][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-24 07:53:36.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:36.486][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.488][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.489][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.490][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:36.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.494][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:36.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.499][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:36.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:36.503][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.505][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.506][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-24 07:53:36.509][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.510][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:53:36.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:36.514][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.517][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.520][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:53:36.521][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:36.523][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.524][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-24 07:53:36.525][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:36.527][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.528][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:36.529][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.531][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:36.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.535][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:36.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:36.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:36.538][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:36.540][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:36.542][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:36.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:36.545][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:36.547][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:36.548][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.595][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[2023-02-24 07:53:36.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.615][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[2023-02-24 07:53:36.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.642][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[2023-02-24 07:53:36.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.655][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[2023-02-24 07:53:36.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.668][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[2023-02-24 07:53:36.670][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-24 07:53:36.673][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-24 07:53:36.675][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-24 07:53:36.677][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-24 07:53:36.679][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:53:36.681][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-24 07:53:36.683][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-24 07:53:36.685][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-24 07:53:36.687][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-24 07:53:36.689][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-24 07:53:36.691][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:53:36.693][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-24 07:53:36.695][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-24 07:53:36.697][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-24 07:53:36.699][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-24 07:53:36.702][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-24 07:53:36.704][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-24 07:53:36.706][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-24 07:53:36.708][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:53:36.710][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-24 07:53:36.712][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-24 07:53:36.714][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-24 07:53:36.717][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-24 07:53:36.719][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-24 07:53:36.721][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-24 07:53:36.723][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-24 07:53:36.725][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-24 07:53:36.727][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-24 07:53:36.730][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-24 07:53:36.732][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-24 07:53:36.735][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-24 07:53:36.737][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-24 07:53:36.740][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-24 07:53:36.742][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-24 07:53:36.745][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-24 07:53:36.748][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-24 07:53:36.750][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-24 07:53:36.753][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-24 07:53:36.756][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-24 07:53:36.758][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-24 07:53:36.761][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-24 07:53:36.764][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-24 07:53:36.766][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-24 07:53:36.769][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-24 07:53:36.772][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-24 07:53:36.774][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-24 07:53:36.777][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-24 07:53:36.779][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-24 07:53:36.782][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-24 07:53:36.785][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-24 07:53:36.787][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-24 07:53:36.790][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-24 07:53:36.792][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-24 07:53:36.795][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-24 07:53:36.797][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-24 07:53:36.800][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-24 07:53:36.803][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-24 07:53:36.805][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-24 07:53:36.808][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-24 07:53:36.811][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-24 07:53:36.813][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-24 07:53:36.816][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-24 07:53:36.860][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-24 07:53:36.862][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-24 07:53:36.864][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-24 07:53:36.866][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-24 07:53:36.868][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:53:36.871][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:53:36.873][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-24 07:53:36.876][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-24 07:53:36.878][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-24 07:53:36.880][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-24 07:53:36.882][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-24 07:53:36.884][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-24 07:53:36.886][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-24 07:53:36.888][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-24 07:53:36.891][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-24 07:53:36.893][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-24 07:53:36.896][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-24 07:53:36.898][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-24 07:53:36.900][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-24 07:53:36.903][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-24 07:53:36.906][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-24 07:53:36.909][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-24 07:53:36.911][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:53:36.913][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:36.914][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.916][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.918][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[2023-02-24 07:53:36.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.927][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[2023-02-24 07:53:36.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.936][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[2023-02-24 07:53:36.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.955][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[2023-02-24 07:53:36.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.974][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[2023-02-24 07:53:36.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.983][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[2023-02-24 07:53:36.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:36.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:36.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:36.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:36.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:36.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:36.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:36.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.047][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[2023-02-24 07:53:37.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.056][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[2023-02-24 07:53:37.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:37.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:37.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:37.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:37.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:37.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:37.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:37.075][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-24 07:53:37.077][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-24 07:53:37.080][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:37.081][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-24 07:53:37.083][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:37.084][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:37.085][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:37.087][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:37.088][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:37.089][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-24 07:53:37.091][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-24 07:53:37.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:37.093][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:37.095][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-24 07:53:37.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-24 07:53:37.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-24 07:53:37.099][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:37.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:37.100][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:37.100][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:37.102][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-24 07:53:37.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:37.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:37.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:37.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:37.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:37.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:37.111][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:37.111][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-24 07:53:37.112][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:37.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:37.114][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:37.116][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-24 07:53:37.116][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-24 07:53:37.117][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:53:37.120][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:53:37.122][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-24 07:53:37.124][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:53:37.126][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:53:37.128][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:53:37.133][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-24 07:53:37.134][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-24 07:53:37.136][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-24 07:53:37.138][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-24 07:53:37.139][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:53:37.141][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:53:37.143][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-24 07:53:37.144][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-24 07:53:37.146][biodb::testThat]
biodb.INFO [2023-02-24 07:53:37.147][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-02-24 07:53:37.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:37.150][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:37.156][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-24 07:53:37.161][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:37.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:37.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-02-24 07:53:38.252][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-02-24 07:53:39.639][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:39.648][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-02-24 07:53:39.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-02-24 07:53:39.671][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[2023-02-24 07:53:39.676][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:39.677][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:39.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:53:40.875][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:53:42.032][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:42.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-02-24 07:53:42.067][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-02-24 07:53:42.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:42.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:42.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:42.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:42.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:42.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:42.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:42.094][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:42.099][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:42.100][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:42.103][private$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[2023-02-24 07:53:43.185][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[2023-02-24 07:53:45.346][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:45.356][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-02-24 07:53:45.372][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-02-24 07:53:45.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.441][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[2023-02-24 07:53:45.446][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:45.448][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-02-24 07:53:45.449][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:45.451][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-02-24 07:53:45.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.471][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[2023-02-24 07:53:45.476][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:45.478][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-02-24 07:53:45.479][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:45.481][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-02-24 07:53:45.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.519][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[2023-02-24 07:53:45.524][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:45.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-02-24 07:53:45.527][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:45.529][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-02-24 07:53:45.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.550][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[2023-02-24 07:53:45.554][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:45.556][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-02-24 07:53:45.558][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:45.560][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-02-24 07:53:45.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:45.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:45.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:45.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:45.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:45.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:45.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:45.580][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[2023-02-24 07:53:45.584][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:45.586][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:45.588][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:53:46.724][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:53:47.886][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:47.896][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-02-24 07:53:47.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-02-24 07:53:47.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:47.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:47.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:47.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:47.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:47.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:47.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-24 07:53:47.938][biodb::testThat]
biodb.INFO [2023-02-24 07:53:47.940][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-02-24 07:53:47.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:47.942][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:47.947][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:47.952][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:47.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:47.957][private$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[2023-02-24 07:53:49.132][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[2023-02-24 07:53:50.263][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:50.273][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-02-24 07:53:50.290][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-02-24 07:53:50.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:50.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:50.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:50.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:50.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:50.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:50.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:50.319][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[2023-02-24 07:53:50.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:50.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:50.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-02-24 07:53:51.514][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-02-24 07:53:52.661][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:52.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-02-24 07:53:52.689][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-02-24 07:53:52.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:52.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:52.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:52.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:52.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:52.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-24 07:53:52.716][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-24 07:53:52.718][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-24 07:53:52.720][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-24 07:53:52.722][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-24 07:53:52.723][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:52.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:52.726][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:52.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:52.729][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-24 07:53:52.738][biodb::testContext]
biodb.INFO [2023-02-24 07:53:52.739][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:53:52.741][biodb::testContext] Test context - Test web services
biodb.INFO [2023-02-24 07:53:52.742][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:53:52.744][biodb::testContext]
biodb.INFO [2023-02-24 07:53:52.750][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:53:52.753][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-24 07:53:52.758][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:52.759][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-24 07:53:52.761][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-24 07:53:52.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.766][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-24 07:53:52.768][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-24 07:53:52.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.773][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-24 07:53:52.775][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-24 07:53:52.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.780][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-24 07:53:52.781][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-24 07:53:52.783][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-24 07:53:52.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.788][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-24 07:53:52.790][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-24 07:53:52.791][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-24 07:53:52.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.797][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-24 07:53:52.798][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-24 07:53:52.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.804][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-24 07:53:52.805][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-24 07:53:52.807][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-24 07:53:52.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.812][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-24 07:53:52.814][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-24 07:53:52.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.819][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-24 07:53:52.821][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-24 07:53:52.822][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-24 07:53:52.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.842][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:53:52.859][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-24 07:53:52.861][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-24 07:53:52.862][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-24 07:53:52.864][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-24 07:53:52.865][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-24 07:53:52.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.871][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-24 07:53:52.872][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-24 07:53:52.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.878][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-24 07:53:52.879][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-24 07:53:52.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.884][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-24 07:53:52.886][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-24 07:53:52.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.891][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-24 07:53:52.893][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-24 07:53:52.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.898][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-24 07:53:52.899][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-24 07:53:52.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.904][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:53:52.906][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-24 07:53:52.910][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-24 07:53:52.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.915][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-24 07:53:52.917][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-24 07:53:52.918][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-24 07:53:52.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:52.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:52.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:52.924][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-24 07:53:52.927][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:52.929][self$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[2023-02-24 07:53:52.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.932][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:52.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:52.936][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:52.938][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:52.939][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:53:52.941][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:52.942][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.944][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-24 07:53:52.945][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:52.947][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:52.948][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.950][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:52.950][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:52.950][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:52.950][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:53:52.950][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:53:52.951][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:52.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:52.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:52.955][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:52.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:52.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:52.959][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:52.961][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:52.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:52.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:52.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:52.967][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:52.968][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-24 07:53:52.971][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:52.972][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:53:52.974][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:52.977][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.978][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:52.980][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:52.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:52.983][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:53:52.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:52.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.987][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-24 07:53:52.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:52.990][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:52.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:52.993][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:52.993][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:52.993][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:52.993][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:53:52.993][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:53:52.995][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:52.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:52.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:52.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:53.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.005][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:53.008][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:53.009][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.011][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.012][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-24 07:53:53.015][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.016][self$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[2023-02-24 07:53:53.018][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:53.021][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.022][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.024][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.025][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.027][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:53:53.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:53.030][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.031][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-24 07:53:53.033][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:53.034][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.036][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.037][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:53.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:53.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.049][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:53.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:53.053][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.055][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.056][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-24 07:53:53.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.061][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:53:53.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:53.065][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.068][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.071][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:53:53.072][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:53.074][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.075][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-24 07:53:53.077][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:53.078][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.080][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.081][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:53.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:53.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.093][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:53.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:53.097][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.098][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:53.100][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:53.101][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.103][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[2023-02-24 07:53:53.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.109][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[2023-02-24 07:53:53.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.122][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[2023-02-24 07:53:53.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.128][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[2023-02-24 07:53:53.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.172][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[2023-02-24 07:53:53.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.179][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[2023-02-24 07:53:53.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.191][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[2023-02-24 07:53:53.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.212][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-24 07:53:53.214][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-24 07:53:53.216][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-24 07:53:53.218][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-24 07:53:53.220][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:53:53.222][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-24 07:53:53.224][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-24 07:53:53.226][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-24 07:53:53.228][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-24 07:53:53.230][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-24 07:53:53.232][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:53:53.234][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-24 07:53:53.236][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-24 07:53:53.238][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-24 07:53:53.240][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-24 07:53:53.241][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-24 07:53:53.243][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-24 07:53:53.245][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-24 07:53:53.247][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:53:53.249][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-24 07:53:53.251][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-24 07:53:53.253][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-24 07:53:53.255][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-24 07:53:53.257][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-24 07:53:53.259][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-24 07:53:53.261][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-24 07:53:53.263][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-24 07:53:53.265][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-24 07:53:53.267][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-24 07:53:53.269][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-24 07:53:53.271][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-24 07:53:53.273][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-24 07:53:53.275][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-24 07:53:53.285][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-24 07:53:53.287][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-24 07:53:53.289][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-24 07:53:53.291][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-24 07:53:53.293][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-24 07:53:53.295][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-24 07:53:53.297][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-24 07:53:53.299][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-24 07:53:53.300][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-24 07:53:53.302][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-24 07:53:53.304][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-24 07:53:53.306][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-24 07:53:53.308][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-24 07:53:53.310][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-24 07:53:53.312][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-24 07:53:53.314][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-24 07:53:53.316][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-24 07:53:53.318][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-24 07:53:53.320][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-24 07:53:53.321][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-24 07:53:53.323][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-24 07:53:53.325][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-24 07:53:53.327][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-24 07:53:53.329][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-24 07:53:53.331][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-24 07:53:53.333][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-24 07:53:53.335][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-24 07:53:53.337][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-24 07:53:53.339][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-24 07:53:53.340][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-24 07:53:53.342][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-24 07:53:53.344][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-24 07:53:53.346][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-24 07:53:53.348][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:53:53.350][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:53:53.352][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-24 07:53:53.354][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-24 07:53:53.355][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-24 07:53:53.357][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-24 07:53:53.359][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-24 07:53:53.361][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-24 07:53:53.363][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-24 07:53:53.365][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-24 07:53:53.367][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-24 07:53:53.369][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-24 07:53:53.371][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-24 07:53:53.372][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-24 07:53:53.374][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-24 07:53:53.376][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-24 07:53:53.378][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-24 07:53:53.380][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-24 07:53:53.382][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:53:53.384][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:53.385][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.387][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.405][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[2023-02-24 07:53:53.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.447][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[2023-02-24 07:53:53.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.456][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.DEBUG[2023-02-24 07:53:53.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.506][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[2023-02-24 07:53:53.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:53.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:53.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:53.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:53.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:53.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:53.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:53.533][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-24 07:53:53.535][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-24 07:53:53.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.539][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.540][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:53.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.545][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.547][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-24 07:53:53.548][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-24 07:53:53.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:53.551][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.552][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-24 07:53:53.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-24 07:53:53.555][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-24 07:53:53.556][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:53.557][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:53.557][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:53.557][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:53.559][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-24 07:53:53.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.563][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:53.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:53.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:53.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:53.568][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:53.568][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-24 07:53:53.570][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:53.571][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:53.572][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:53.574][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-24 07:53:53.574][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-24 07:53:53.576][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:53:53.578][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:53:53.580][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-24 07:53:53.582][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:53:53.585][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:53:53.587][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:53:53.592][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-24 07:53:53.593][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-24 07:53:53.595][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-24 07:53:53.597][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-24 07:53:53.599][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:53:53.600][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:53:53.602][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-24 07:53:53.604][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-24 07:53:53.605][biodb::testThat]
biodb.INFO [2023-02-24 07:53:53.607][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-02-24 07:53:53.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:53.609][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:53.614][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-24 07:53:53.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:53.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-02-24 07:53:53.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:53.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-02-24 07:53:53.630][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-02-24 07:53:53.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:53.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:53.639][private$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[2023-02-24 07:53:54.755][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[2023-02-24 07:53:56.165][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:53:56.174][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-02-24 07:53:56.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-02-24 07:53:56.198][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-24 07:53:56.200][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-24 07:53:56.201][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-24 07:53:56.203][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-24 07:53:56.204][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.206][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.209][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-24 07:53:56.215][biodb::testContext]
biodb.INFO [2023-02-24 07:53:56.217][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:53:56.218][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-02-24 07:53:56.219][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-24 07:53:56.221][biodb::testContext]
biodb.INFO [2023-02-24 07:53:56.227][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:53:56.229][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-24 07:53:56.233][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:56.235][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-24 07:53:56.236][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-24 07:53:56.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.241][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-24 07:53:56.243][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-24 07:53:56.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.248][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-24 07:53:56.250][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-24 07:53:56.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.255][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-24 07:53:56.256][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-24 07:53:56.258][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-24 07:53:56.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.263][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-24 07:53:56.264][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-24 07:53:56.265][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-24 07:53:56.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.270][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-24 07:53:56.272][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-24 07:53:56.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.277][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-24 07:53:56.278][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-24 07:53:56.279][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-24 07:53:56.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.284][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-24 07:53:56.286][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-24 07:53:56.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.290][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[2023-02-24 07:53:56.291][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-24 07:53:56.292][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-24 07:53:56.294][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-24 07:53:56.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.299][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:53:56.301][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-24 07:53:56.302][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-24 07:53:56.304][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-24 07:53:56.305][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-24 07:53:56.307][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-24 07:53:56.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.312][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-24 07:53:56.313][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-24 07:53:56.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.318][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-24 07:53:56.320][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-24 07:53:56.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.325][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-24 07:53:56.326][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-24 07:53:56.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.331][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-24 07:53:56.333][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-24 07:53:56.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.338][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-24 07:53:56.339][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-24 07:53:56.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.344][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-24 07:53:56.346][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-24 07:53:56.350][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-24 07:53:56.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.354][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.DEBUG[2023-02-24 07:53:56.355][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-24 07:53:56.356][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-24 07:53:56.358][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-24 07:53:56.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.363][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-24 07:53:56.366][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.367][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-24 07:53:56.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.370][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:56.371][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.374][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.377][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:53:56.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:56.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.381][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-24 07:53:56.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:56.384][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.386][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.387][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:56.387][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:56.387][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:56.387][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:53:56.387][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:53:56.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:56.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:56.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.398][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:56.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:56.401][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.403][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.404][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-24 07:53:56.407][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.408][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:53:56.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.411][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:56.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.415][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.418][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:53:56.419][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:56.420][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.422][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-24 07:53:56.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:56.425][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:56.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:56.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:56.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-24 07:53:56.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-24 07:53:56.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:56.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.433][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:56.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.437][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.438][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:56.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:56.442][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.443][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.445][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-24 07:53:56.447][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.449][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-24 07:53:56.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.452][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:56.453][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.458][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-24 07:53:56.460][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:56.461][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.463][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-24 07:53:56.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:56.465][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.467][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.468][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.469][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:56.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:56.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.478][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.480][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:56.481][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:56.482][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.484][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.485][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-24 07:53:56.488][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.489][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-24 07:53:56.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:56.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.495][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.496][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.498][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.499][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-24 07:53:56.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:56.502][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.503][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-24 07:53:56.505][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:56.506][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.507][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.509][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.510][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-24 07:53:56.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.514][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:56.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:56.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:56.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.519][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:56.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:56.523][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.525][self$setPropertyValue]
biodb.DEBUG[2023-02-24 07:53:56.526][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:56.528][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.603][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.DEBUG[2023-02-24 07:53:56.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.609][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[2023-02-24 07:53:56.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.649][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-24 07:53:56.651][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-24 07:53:56.653][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-24 07:53:56.655][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-24 07:53:56.657][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:53:56.658][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-24 07:53:56.660][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-24 07:53:56.662][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-24 07:53:56.664][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-24 07:53:56.666][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-24 07:53:56.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:53:56.670][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-24 07:53:56.672][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-24 07:53:56.674][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-24 07:53:56.676][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-24 07:53:56.678][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-24 07:53:56.680][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-24 07:53:56.682][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-24 07:53:56.684][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:53:56.686][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-24 07:53:56.688][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-24 07:53:56.690][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-24 07:53:56.691][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-24 07:53:56.693][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-24 07:53:56.695][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-24 07:53:56.697][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-24 07:53:56.699][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-24 07:53:56.701][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-24 07:53:56.703][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-24 07:53:56.705][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-24 07:53:56.707][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-24 07:53:56.709][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-24 07:53:56.711][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-24 07:53:56.713][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-24 07:53:56.715][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-24 07:53:56.717][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-24 07:53:56.719][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-24 07:53:56.721][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-24 07:53:56.723][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-24 07:53:56.725][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-24 07:53:56.727][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-24 07:53:56.729][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-24 07:53:56.730][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-24 07:53:56.732][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-24 07:53:56.734][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-24 07:53:56.736][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-24 07:53:56.738][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-24 07:53:56.740][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-24 07:53:56.743][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-24 07:53:56.745][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-24 07:53:56.747][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-24 07:53:56.749][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-24 07:53:56.751][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-24 07:53:56.753][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-24 07:53:56.754][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-24 07:53:56.756][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-24 07:53:56.758][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-24 07:53:56.760][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-24 07:53:56.762][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-24 07:53:56.764][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-24 07:53:56.766][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-24 07:53:56.768][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-24 07:53:56.770][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-24 07:53:56.772][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-24 07:53:56.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-24 07:53:56.776][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-24 07:53:56.778][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:53:56.780][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:53:56.782][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-24 07:53:56.784][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-24 07:53:56.786][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-24 07:53:56.788][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-24 07:53:56.790][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-24 07:53:56.792][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-24 07:53:56.794][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-24 07:53:56.796][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-24 07:53:56.798][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-24 07:53:56.800][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-24 07:53:56.802][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-24 07:53:56.804][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-24 07:53:56.806][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-24 07:53:56.808][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-24 07:53:56.810][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-24 07:53:56.812][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-24 07:53:56.814][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-24 07:53:56.815][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-24 07:53:56.817][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.819][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.908][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[2023-02-24 07:53:56.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.943][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[2023-02-24 07:53:56.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-24 07:53:56.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:56.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:56.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:56.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:56.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:56.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:56.980][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-02-24 07:53:56.982][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-02-24 07:53:56.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:56.986][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.988][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.989][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-24 07:53:56.996][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:56.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-24 07:53:56.999][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:57.001][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-02-24 07:53:57.003][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-24 07:53:57.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-24 07:53:57.006][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:57.007][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-02-24 07:53:57.009][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-02-24 07:53:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-02-24 07:53:57.012][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-24 07:53:57.014][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-24 07:53:57.014][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-24 07:53:57.014][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-24 07:53:57.015][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-24 07:53:57.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:57.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:57.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-24 07:53:57.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-24 07:53:57.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-24 07:53:57.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-24 07:53:57.026][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:57.026][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-02-24 07:53:57.027][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-24 07:53:57.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-24 07:53:57.030][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-24 07:53:57.032][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-02-24 07:53:57.032][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-02-24 07:53:57.034][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-24 07:53:57.036][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-24 07:53:57.039][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-02-24 07:53:57.041][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-24 07:53:57.043][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-24 07:53:57.046][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-24 07:53:57.052][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-02-24 07:53:57.053][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-02-24 07:53:57.055][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-02-24 07:53:57.057][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-02-24 07:53:57.059][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:53:57.061][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-24 07:53:57.063][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-02-24 07:53:57.064][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-02-24 07:53:57.066][biodb::testThat]
biodb.INFO [2023-02-24 07:53:57.068][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-02-24 07:53:57.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-24 07:53:57.071][biodb::testThat]
biodb.DEBUG[2023-02-24 07:53:57.076][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-02-24 07:53:57.082][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:57.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-02-24 07:53:57.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:57.089][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-02-24 07:53:57.094][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[2023-02-24 07:53:57.098][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-24 07:53:57.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-02-24 07:53:57.102][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-24 07:53:57.104][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-02-24 07:53:57.109][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-02-24 07:53:57.110][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-24 07:53:57.113][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-02-24 07:53:57.115][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-24 07:53:57.116][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-24 07:53:57.118][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-02-24 07:53:57.119][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-02-24 07:53:57.121][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-24 07:53:57.122][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-24 07:53:57.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:53:57.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:53:57.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:53:57.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:53:57.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:53:57.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:53:57.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-24 07:53:57.145][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-02-24 07:53:57.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-24 07:53:57.151][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-24 07:53:57.152][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-02-24 07:53:59.964][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-02-24 07:54:02.725][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-24 07:54:02.736][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-02-24 07:54:02.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-02-24 07:54:02.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-02-24 07:54:02.773][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-24 07:54:02.795][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-02-24 07:54:02.797][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-02-24 07:54:02.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-24 07:54:02.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:54:02.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:54:02.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:54:02.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:54:02.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:54:02.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-24 07:54:02.820][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:02.822][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:02.823][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.825][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:02.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.837][ef$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:54:02.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:54:02.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.841][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-02-24 07:54:02.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-02-24 07:54:02.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.854][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:54:02.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:54:02.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.858][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-24 07:54:02.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-24 07:54:02.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.870][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-24 07:54:02.872][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-24 07:54:02.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.874][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.876][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-24 07:54:02.878][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-24 07:54:02.879][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.881][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.883][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:54:02.884][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:54:02.886][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.887][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.890][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:54:02.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-24 07:54:02.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.900][ef$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:54:02.902][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:54:02.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.904][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.907][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-02-24 07:54:02.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-24 07:54:02.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:54:02.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:54:02.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.921][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:54:02.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-24 07:54:02.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.933][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:54:02.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:54:02.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.956][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-24 07:54:02.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-24 07:54:02.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.968][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:54:02.970][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:54:02.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.972][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.974][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-02-24 07:54:02.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-02-24 07:54:02.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.984][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:54:02.986][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:54:02.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.988][ef$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:02.990][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-24 07:54:02.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-24 07:54:02.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:02.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:54:03.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:54:03.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:54:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:54:03.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-24 07:54:03.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-24 07:54:03.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-24 07:54:03.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-24 07:54:03.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-24 07:54:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-24 07:54:03.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-24 07:54:03.060][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-02-24 07:54:03.062][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-24 07:54:03.063][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-02-24 07:54:03.065][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-02-24 07:54:03.066][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-24 07:54:03.067][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-24 07:54:03.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-24 07:54:03.070][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-24 07:54:03.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-24 07:54:03.073][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-24 07:54:03.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
>
> proc.time()
user system elapsed
32.310 9.962 182.740
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.940 | 0.158 | 6.518 | |
| ChebiEntry | 0.504 | 0.004 | 0.508 | |