| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 194/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.5.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: biodbChebi |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbChebi_1.5.0.tar.gz |
| StartedAt: 2023-04-12 04:57:53 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:00:20 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 146.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbChebi_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbChebi.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2023-04-12 04:58:40.347][biodb::testContext]
biodb.INFO [2023-04-12 04:58:40.349][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:40.350][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-12 04:58:40.352][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:40.353][biodb::testContext]
biodb.INFO [2023-04-12 04:58:40.370][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:40.373][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:40.381][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:40.383][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:58:40.384][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:58:40.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.388][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:58:40.408][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:58:40.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.412][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:58:40.414][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:58:40.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.417][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:58:40.419][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:58:40.420][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:58:40.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.424][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:58:40.425][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:58:40.426][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:58:40.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.430][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:58:40.431][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:58:40.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.435][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:58:40.436][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:58:40.437][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:58:40.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.441][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:58:40.442][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:58:40.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:58:40.447][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:58:40.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:58:40.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.452][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:40.453][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:58:40.454][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:58:40.455][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:58:40.456][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:58:40.457][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:58:40.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.461][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:58:40.462][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:58:40.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.466][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:58:40.467][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:58:40.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.471][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:58:40.472][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:58:40.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.476][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:58:40.477][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:58:40.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.481][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:58:40.482][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:58:40.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.486][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:40.487][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:58:40.492][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:58:40.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.497][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:58:40.498][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:58:40.499][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:58:40.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.506][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:58:40.544][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.575][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:58:40.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:40.579][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.581][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.582][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.583][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:40.584][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:40.585][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.586][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:58:40.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:40.588][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:40.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:40.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:40.590][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:40.590][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:40.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:40.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:40.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.598][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:40.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:40.602][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.603][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.604][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:58:40.606][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.607][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:40.608][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:40.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.612][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.613][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.614][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:40.615][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:40.616][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.617][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:58:40.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:40.619][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.621][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:40.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:40.621][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:40.621][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:40.621][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:40.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:40.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:40.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.630][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:40.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:40.633][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.634][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.635][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:58:40.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.638][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:58:40.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:40.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.645][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:40.646][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:40.647][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.648][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:58:40.649][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:40.650][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.651][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.652][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.653][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:40.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.656][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:40.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.660][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:40.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:40.663][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.664][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.665][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:58:40.667][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.668][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:40.669][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.670][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:40.671][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.675][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:40.676][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:40.677][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.678][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:58:40.679][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:40.680][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.681][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:40.682][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.683][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:40.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.686][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:40.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:40.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:40.689][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:40.690][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:40.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:40.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:40.694][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:40.699][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:40.700][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.730][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.DEBUG[2023-04-12 04:58:40.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.735][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[2023-04-12 04:58:40.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.751][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[2023-04-12 04:58:40.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.760][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[2023-04-12 04:58:40.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.765][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[2023-04-12 04:58:40.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.787][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:58:40.793][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:58:40.795][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:58:40.797][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:58:40.799][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:58:40.801][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:40.802][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:40.804][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:40.806][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:58:40.808][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:40.809][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:40.811][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:58:40.813][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:40.814][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:40.816][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:58:40.818][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:40.819][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:58:40.821][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:58:40.822][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:58:40.824][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:58:40.826][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:58:40.827][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:58:40.829][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:58:40.830][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:58:40.832][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:58:40.833][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:58:40.844][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:58:40.846][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:58:40.848][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:58:40.850][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:58:40.851][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:58:40.853][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:58:40.854][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:58:40.855][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:58:40.857][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:58:40.858][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:58:40.860][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:58:40.861][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:58:40.863][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:58:40.864][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:58:40.866][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:58:40.867][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:58:40.868][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:58:40.870][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:58:40.871][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:58:40.873][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:58:40.874][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:58:40.876][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:58:40.877][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:58:40.879][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:58:40.880][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:58:40.881][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:58:40.883][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:58:40.884][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:58:40.886][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:58:40.887][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:58:40.889][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:58:40.890][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:58:40.892][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:58:40.893][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:58:40.895][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:58:40.896][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:58:40.897][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:58:40.899][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:58:40.900][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:58:40.902][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:58:40.904][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:58:40.905][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:58:40.906][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:58:40.908][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:58:40.909][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:58:40.911][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:58:40.912][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:58:40.914][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:58:40.915][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:58:40.917][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:58:40.918][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:58:40.919][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:58:40.921][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:58:40.922][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:58:40.924][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:58:40.925][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:58:40.926][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:58:40.934][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:58:40.936][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:40.940][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:40.941][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.943][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.955][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[2023-04-12 04:58:40.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.961][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[2023-04-12 04:58:40.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.992][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[2023-04-12 04:58:40.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:40.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:40.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:40.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:40.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:40.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:40.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:40.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.011][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[2023-04-12 04:58:41.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.030][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[2023-04-12 04:58:41.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:41.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:41.057][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:41.067][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-12 04:58:41.070][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:41.071][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:58:41.072][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:41.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:41.074][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:41.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:41.076][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:41.077][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-12 04:58:41.078][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:58:41.079][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:41.080][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:41.081][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-12 04:58:41.082][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-12 04:58:41.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-12 04:58:41.084][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:41.085][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:41.085][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:41.085][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:41.086][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:58:41.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:41.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:41.089][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:41.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:41.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:41.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:41.093][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:41.093][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-12 04:58:41.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:41.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:41.105][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:41.106][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-12 04:58:41.106][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-12 04:58:41.112][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:58:41.114][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:41.116][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-12 04:58:41.118][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:58:41.120][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:58:41.121][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:58:41.150][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-12 04:58:41.152][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-12 04:58:41.157][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-12 04:58:41.162][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-12 04:58:41.167][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:41.169][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:41.171][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-12 04:58:41.172][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-12 04:58:41.193][biodb::testThat]
biodb.INFO [2023-04-12 04:58:41.195][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-12 04:58:41.196][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:41.197][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:41.201][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-04-12 04:58:41.207][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:41.212][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:41.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:41.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:41.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:41.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:41.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:41.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:41.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:41.255][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.256][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.258][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.259][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.284][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.286][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.288][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.326][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.327][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:41.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:41.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.352][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.354][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.356][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.366][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:41.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:41.368][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.369][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:41.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.379][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:41.380][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.383][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.393][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.397][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.406][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.408][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.409][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.419][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:41.420][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.422][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.424][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:41.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.449][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:41.451][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:41.452][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.453][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.455][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:41.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:41.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:41.549][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-04-12 04:58:41.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:41.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:41.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:41.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:41.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:41.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:41.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:41.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.614][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:41.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:41.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.618][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:41.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:41.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.622][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:41.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:41.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.750][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.752][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.753][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:41.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:41.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.780][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.781][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.783][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:41.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.807][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.809][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.810][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:41.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:41.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.835][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.838][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:41.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:41.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.863][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.865][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.866][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.867][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:41.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.899][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:41.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.963][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.968][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.969][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.971][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.972][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:41.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:41.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.985][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.994][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:41.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:41.998][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-12 04:58:41.999][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.001][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.014][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.023][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.027][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.028][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.029][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.030][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.031][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.043][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.048][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.052][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.056][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.057][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.058][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.059][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.060][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.085][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.087][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.088][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.114][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.117][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.131][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.133][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.135][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.140][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:42.142][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:42.143][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.144][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.149][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:42.151][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:42.151][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.153][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.158][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.159][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.160][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.161][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.168][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.170][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.175][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.177][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.178][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.179][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.184][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:42.185][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:42.186][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.187][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:42.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:42.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.201][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.207][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.208][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.210][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.215][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.217][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.219][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.224][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.225][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.226][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.227][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:42.234][biodb::testThat]
biodb.INFO [2023-04-12 04:58:42.235][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-12 04:58:42.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:42.237][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:42.251][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-04-12 04:58:42.259][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:42.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-04-12 04:58:42.265][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:42.266][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-04-12 04:58:42.268][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:42.312][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:42.313][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:42.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:42.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:42.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:42.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:42.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:42.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:42.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:42.328][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.329][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.354][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:42.355][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:42.356][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.357][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.358][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:42.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:42.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.365][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:42.366][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:42.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.368][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.376][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.378][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.380][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.388][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.389][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.390][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.391][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:42.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.400][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.401][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.403][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.405][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:42.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.419][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:42.420][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:42.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.422][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.431][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:42.432][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:42.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.434][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:42.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.442][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.444][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.445][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.454][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:42.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.457][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.458][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.459][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:42.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:42.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.466][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.467][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.468][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.469][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.471][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:42.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:42.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:42.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:42.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:42.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:42.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:42.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:42.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:42.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:42.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:42.520][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-04-12 04:58:42.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-12 04:58:42.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-12 04:58:42.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-12 04:58:42.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-12 04:58:42.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-12 04:58:42.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-12 04:58:42.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:42.538][biodb::testThat]
biodb.INFO [2023-04-12 04:58:42.539][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-12 04:58:42.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:42.541][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:42.544][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.546][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.547][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.547][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:42.549][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-04-12 04:58:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:42.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:42.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:42.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:42.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:42.589][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-04-12 04:58:42.602][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-12 04:58:42.629][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:42.644][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-12 04:58:42.646][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:42.647][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-12 04:58:42.670][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:42.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:42.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:42.677][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:58:43.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:58:44.007][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:44.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-04-12 04:58:44.056][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-04-12 04:58:44.064][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-04-12 04:58:44.087][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:44.089][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:44.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.092][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.093][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.095][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.098][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:44.101][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.103][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-12 04:58:44.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:44.106][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:44.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:44.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:44.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:44.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:44.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:44.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:44.293][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:44.295][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-12 04:58:44.297][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:44.298][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-04-12 04:58:44.315][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.317][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-12 04:58:44.318][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:44.319][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:44.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:44.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:44.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:44.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:44.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:44.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:44.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.399][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:44.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:44.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:44.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:44.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:44.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:44.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:44.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:44.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.457][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:44.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:44.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:44.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:44.490][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:44.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:44.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:44.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:44.498][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.499][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-12 04:58:44.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:44.501][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.507][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.509][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-12 04:58:44.510][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:44.511][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.518][biodb::testThat]
biodb.INFO [2023-04-12 04:58:44.519][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-12 04:58:44.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:44.521][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:44.525][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-04-12 04:58:45.087][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-04-12 04:58:46.334][biodb::testThat]
biodb.INFO [2023-04-12 04:58:46.336][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-12 04:58:46.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:46.339][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:46.817][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2023-04-12 04:58:47.485][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:47.488][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:47.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.491][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.492][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:47.494][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:47.495][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.497][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:47.499][biodb::testThat]
biodb.INFO [2023-04-12 04:58:47.501][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-04-12 04:58:47.502][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:47.503][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:47.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:47.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:47.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:47.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:47.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:47.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:47.640][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:47.643][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:47.645][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-12 04:58:47.646][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:47.647][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-12 04:58:47.720][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:47.723][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:47.725][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-12 04:58:47.726][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:47.728][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-04-12 04:58:47.743][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:47.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:47.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:47.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:47.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:47.821][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:47.825][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:47.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-12 04:58:47.827][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:47.829][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-12 04:58:47.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:47.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:47.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:47.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:47.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:47.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:47.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:47.842][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-04-12 04:58:47.886][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:47.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-04-12 04:58:47.889][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:47.891][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:47.892][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:47.893][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:47.894][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:47.895][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:47.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:47.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:47.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:47.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:47.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:47.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:47.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:47.910][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-04-12 04:58:47.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:47.927][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:47.948][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-04-12 04:58:48.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-04-12 04:58:48.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:48.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-04-12 04:58:48.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-04-12 04:58:48.888][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-04-12 04:58:48.895][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:48.925][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:48.927][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:48.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:48.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:48.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:48.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:48.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:48.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:48.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:48.950][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:48.951][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:48.953][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:48.954][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:48.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:48.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:48.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:48.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:48.967][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:48.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:48.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:48.971][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:48.973][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:48.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:48.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:48.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:48.983][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:48.985][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:48.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:48.988][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:48.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:48.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:48.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:48.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:49.003][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:49.005][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.006][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:49.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:49.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.019][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:49.021][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:49.022][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.024][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.026][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:49.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:49.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.051][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:49.053][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:49.055][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.056][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.058][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:49.059][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.060][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.062][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.063][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:49.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:49.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:49.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.077][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:49.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:49.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.089][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:49.090][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:49.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.093][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:49.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.105][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:49.107][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:49.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.110][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.112][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:49.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:49.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.122][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:49.124][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:49.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.127][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:49.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:49.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:49.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:49.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:49.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:49.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:49.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:49.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:49.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:49.205][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-04-12 04:58:49.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:49.241][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:49.246][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:49.248][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-12 04:58:49.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:49.252][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-12 04:58:49.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:49.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:49.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:49.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:49.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:49.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:49.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:49.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:49.323][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:49.328][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:49.330][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-12 04:58:49.331][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:49.333][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-12 04:58:49.398][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:58:49.403][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:49.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-12 04:58:49.408][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:49.410][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-12 04:58:49.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:49.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:49.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:49.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:49.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:49.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:49.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:49.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:49.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:49.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:49.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:49.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:49.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:49.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:49.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:49.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:49.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:49.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:49.477][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-04-12 04:58:49.478][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:49.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-04-12 04:58:49.481][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:49.482][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:49.484][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:49.485][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:49.486][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:49.487][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:49.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:49.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:49.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:49.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:49.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:49.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:49.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:49.515][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-04-12 04:58:49.518][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:49.519][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:49.520][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-04-12 04:58:49.968][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-04-12 04:58:50.445][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:50.459][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-04-12 04:58:50.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-04-12 04:58:50.499][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-04-12 04:58:50.506][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:50.539][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:50.542][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:50.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:50.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:50.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:50.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:50.566][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.569][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.571][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.584][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:50.586][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:50.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.589][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.591][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:50.593][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:50.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.596][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.598][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:50.599][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:50.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.602][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:50.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:50.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.608][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.610][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:50.612][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:50.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.615][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.617][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:50.618][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.621][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.623][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:50.625][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:50.627][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.628][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.630][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:50.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:50.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:50.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:50.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.648][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:50.650][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:50.652][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.653][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.655][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:50.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:50.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.666][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:50.668][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:50.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.671][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:50.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:50.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:50.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:50.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:50.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:50.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:50.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:50.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:50.760][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-04-12 04:58:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:50.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:50.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:50.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:50.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:50.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:50.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:50.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.815][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-04-12 04:58:50.817][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:50.820][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-04-12 04:58:50.822][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:50.824][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:50.825][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:50.827][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:50.829][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:50.830][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:50.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:50.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:50.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:50.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.853][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-04-12 04:58:50.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:50.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:50.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-04-12 04:58:51.318][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-04-12 04:58:51.834][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:51.845][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-04-12 04:58:51.861][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-04-12 04:58:51.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-04-12 04:58:51.891][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:51.925][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:51.928][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:51.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:51.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:51.948][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.951][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.959][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:51.960][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:51.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.962][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.964][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:51.965][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:51.966][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.967][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.968][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:51.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:51.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.971][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.973][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.974][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.975][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.977][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.978][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.979][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.980][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.981][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:51.982][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:51.983][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.984][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.986][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.988][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.989][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.992][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.001][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:52.002][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:52.003][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.004][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.005][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.012][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.013][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.014][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.015][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:52.058][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-04-12 04:58:52.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:52.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:52.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:52.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:52.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:52.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:52.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:52.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.110][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-04-12 04:58:52.111][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:52.113][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-04-12 04:58:52.115][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:52.116][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:52.117][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:52.118][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:52.119][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:52.121][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:52.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:52.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:52.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:52.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:52.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:52.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.137][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-04-12 04:58:52.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:52.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:52.143][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-04-12 04:58:52.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-04-12 04:58:53.112][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:53.121][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-04-12 04:58:53.134][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-04-12 04:58:53.146][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-04-12 04:58:53.152][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:53.189][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:53.192][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:53.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:53.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:53.222][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.224][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.226][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.228][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.243][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:53.245][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:53.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.249][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.251][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.253][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.255][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.256][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.259][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:53.260][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:53.262][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.263][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.265][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.266][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.268][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.289][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.291][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.292][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.293][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.294][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.296][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:53.297][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.299][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.300][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.301][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.302][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.303][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.304][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.306][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.307][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.308][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.318][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:53.320][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:53.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.322][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.323][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:53.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:53.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.330][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:53.331][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:53.332][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.333][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.379][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-04-12 04:58:53.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:53.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:53.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.412][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-04-12 04:58:53.413][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:53.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-04-12 04:58:53.416][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:53.417][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:53.418][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:53.419][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:53.420][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:53.421][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:53.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:53.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.435][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-04-12 04:58:53.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:53.439][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:53.441][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-04-12 04:58:54.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-04-12 04:58:54.605][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:54.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-04-12 04:58:54.636][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-04-12 04:58:54.649][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-04-12 04:58:54.655][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:54.675][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:54.677][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:54.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:54.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:54.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:54.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:54.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:54.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:54.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:54.692][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.695][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.704][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:54.705][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:54.706][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.707][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.708][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:54.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:54.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.716][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:54.717][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:54.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.719][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.720][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:54.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:54.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.728][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:54.729][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:54.730][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.731][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:54.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:54.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.740][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:54.741][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:54.742][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.743][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.752][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:54.753][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:54.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.755][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:54.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:54.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.763][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:54.764][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.766][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.775][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.776][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.778][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.786][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.798][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.806][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:54.808][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:54.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.809][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.811][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:54.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:54.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.817][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:54.819][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:54.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.820][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.872][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-04-12 04:58:54.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:54.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:54.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:54.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:54.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:54.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:54.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:54.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:54.897][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-04-12 04:58:54.899][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:54.900][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-04-12 04:58:54.902][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:54.903][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:54.904][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:54.905][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:54.906][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:54.907][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:54.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:54.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:54.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:54.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:54.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:54.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:54.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:54.922][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-04-12 04:58:54.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:54.926][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:54.928][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-04-12 04:58:55.415][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-04-12 04:58:55.923][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:55.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-04-12 04:58:55.949][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-04-12 04:58:55.963][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-04-12 04:58:55.971][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:55.999][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:56.000][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:56.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:56.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:56.014][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.017][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.025][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:56.026][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:56.027][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.027][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.029][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:56.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:56.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.035][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:56.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:56.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.038][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:56.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:56.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.047][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:56.048][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:56.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.050][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:56.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:56.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.058][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:56.059][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:56.060][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.061][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:56.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.068][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:56.069][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:56.070][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.071][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:56.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:56.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.079][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:56.081][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.082][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.082][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.084][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:56.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:56.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:56.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.094][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:56.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:56.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.102][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:56.104][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:56.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.105][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:56.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:56.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.115][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:56.116][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:56.117][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.118][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.119][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:56.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.132][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:56.133][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:56.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.135][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:56.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:56.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:56.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:56.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:56.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:56.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:56.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:56.184][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-04-12 04:58:56.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:56.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:56.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:56.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.208][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-04-12 04:58:56.209][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:56.210][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-04-12 04:58:56.212][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:56.213][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:56.214][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:56.215][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:56.216][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:56.217][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:56.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:56.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.232][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-04-12 04:58:56.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:56.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:56.237][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-04-12 04:58:56.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-04-12 04:58:57.246][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:57.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-04-12 04:58:57.318][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-04-12 04:58:57.335][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-04-12 04:58:57.343][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:57.364][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:57.366][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:57.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:57.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:57.381][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.382][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.383][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.384][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.392][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:57.393][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:57.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.396][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:57.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:57.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.403][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.406][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.414][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.415][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.417][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.425][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.427][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.429][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.437][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.440][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.442][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:57.443][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.444][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.445][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.453][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.454][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.455][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.456][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.464][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.465][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.467][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.476][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:57.477][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:57.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.478][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.480][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:57.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:57.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.488][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.489][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:57.547][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-04-12 04:58:57.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:57.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:57.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:57.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.572][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-04-12 04:58:57.573][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:57.574][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-04-12 04:58:57.576][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:57.577][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:57.578][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:57.579][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:57.580][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:57.581][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:57.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:57.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.596][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-04-12 04:58:57.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:57.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:57.601][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-04-12 04:58:58.051][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-04-12 04:58:58.507][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:58.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-04-12 04:58:58.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-04-12 04:58:58.553][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-04-12 04:58:58.559][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:58.601][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:58.603][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:58.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:58.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:58.624][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.625][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.627][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.635][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:58.636][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:58.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.638][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.639][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:58.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:58.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.646][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.647][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.649][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.657][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.658][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.660][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.670][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.671][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.679][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.680][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.681][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.682][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.683][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:58.684][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.685][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.686][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.688][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:58.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.695][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.696][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.698][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.706][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.709][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.718][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:58.719][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:58.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.721][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.722][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:58.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:58.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:58.730][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:58.731][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.732][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:58.790][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-04-12 04:58:58.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:58.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:58.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.814][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-04-12 04:58:58.815][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:58.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-04-12 04:58:58.818][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:58.819][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:58.820][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:58.821][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:58:58.822][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:58:58.823][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:58:58.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:58.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.838][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-04-12 04:58:58.841][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:58.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:58.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-04-12 04:58:59.285][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-04-12 04:58:59.734][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:59.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-04-12 04:58:59.775][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-04-12 04:58:59.793][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-04-12 04:58:59.801][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:58:59.825][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:59.826][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:58:59.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:59.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:59.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:59.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:59.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:59.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:59.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:59.842][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.858][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.864][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.874][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:59.876][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:59.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.878][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.879][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:58:59.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:58:59.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.887][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.888][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.890][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.900][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.901][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.910][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.911][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.912][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.913][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.922][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.923][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.925][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.926][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:59.927][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:59.928][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.929][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.930][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:58:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.938][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.941][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.949][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.950][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.952][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.961][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:59.962][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:59.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.964][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:58:59.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:58:59.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.973][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.975][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.977][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:00.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:00.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:00.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:00.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:00.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:00.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:00.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:00.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:00.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:00.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:00.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:00.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:00.045][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-04-12 04:59:00.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:00.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:00.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:00.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:00.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:00.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:00.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:00.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:00.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:00.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:00.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:00.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:00.088][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-04-12 04:59:00.089][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:00.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-04-12 04:59:00.093][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:00.095][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:00.096][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:00.098][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:00.099][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:00.101][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:00.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:00.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:00.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:00.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:00.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:00.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:00.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:00.122][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-04-12 04:59:00.125][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:00.126][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:00.127][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-04-12 04:59:00.562][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-04-12 04:59:01.020][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:01.028][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-04-12 04:59:01.041][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-04-12 04:59:01.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-04-12 04:59:01.057][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:01.078][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:01.079][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:01.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:01.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:01.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:01.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:01.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:01.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:01.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:01.094][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.097][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.105][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:01.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:01.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.108][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:01.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:01.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.117][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:01.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:01.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.120][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:01.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:01.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.139][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:01.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:01.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.143][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:01.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:01.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.151][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:01.152][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:01.153][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.154][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:01.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:01.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.162][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:01.164][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:01.165][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.166][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.167][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:01.168][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.170][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.171][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:01.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.179][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:01.180][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:01.181][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.182][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:01.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:01.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.191][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:01.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:01.193][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.194][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:01.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:01.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.204][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:01.205][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:01.206][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.207][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.208][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:01.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:01.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.216][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:01.217][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:01.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.219][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.220][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:01.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:01.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:01.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:01.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:01.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:01.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:01.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:01.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:01.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:01.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:01.274][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-04-12 04:59:01.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:01.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:01.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:01.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:01.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:01.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:01.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:01.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:01.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:01.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:01.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:01.299][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-04-12 04:59:01.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:01.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-04-12 04:59:01.303][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:01.304][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:01.305][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:01.306][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:01.307][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:01.308][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:01.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:01.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:01.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:01.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:01.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:01.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:01.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:01.329][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-04-12 04:59:01.332][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:01.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:01.334][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-04-12 04:59:01.782][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-04-12 04:59:02.244][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:02.256][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-04-12 04:59:02.274][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-04-12 04:59:02.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-04-12 04:59:02.298][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:02.328][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:02.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:02.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:02.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:02.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:02.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:02.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:02.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:02.354][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[2023-04-12 04:59:02.357][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.358][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.359][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.360][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.368][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:02.369][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:02.370][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.371][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.373][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:02.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:02.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.380][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:02.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:02.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.383][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.385][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:02.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:02.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:02.393][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:02.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.404][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:02.405][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:02.406][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.407][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:02.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:02.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.426][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:02.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:02.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.429][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.431][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:02.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.434][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.435][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:02.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:02.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:02.444][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.445][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:02.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:02.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.454][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:02.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:02.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.457][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:02.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:02.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.465][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:02.467][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:02.468][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.469][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:02.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:02.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:02.479][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:02.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.481][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.483][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:02.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:02.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:02.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:02.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:02.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:02.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:02.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:02.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:02.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:02.538][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-04-12 04:59:02.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:02.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:02.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:02.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:02.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:02.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:02.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:02.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:02.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:02.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:02.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:02.564][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-04-12 04:59:02.565][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:02.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-04-12 04:59:02.569][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:02.570][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:02.571][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:02.572][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:02.573][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:02.574][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:02.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:02.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:02.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:02.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:02.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:02.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:02.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:02.590][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-04-12 04:59:02.594][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:02.595][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:02.596][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-04-12 04:59:03.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-04-12 04:59:03.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:03.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-04-12 04:59:03.522][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-04-12 04:59:03.538][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-04-12 04:59:03.544][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:03.575][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:03.577][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:03.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:03.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:03.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:03.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:03.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:03.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:03.596][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.TRACE[2023-04-12 04:59:03.599][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.602][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.604][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.618][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:03.619][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:03.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.621][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.622][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:03.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:03.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.629][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:03.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:03.631][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.632][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:03.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.640][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:03.641][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:03.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.643][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.644][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:03.645][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:03.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.647][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.648][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:03.649][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:03.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.651][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.652][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:03.653][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.655][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.656][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:03.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.662][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:03.663][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:03.664][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.665][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:03.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:03.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.673][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:03.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:03.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.676][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:03.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:03.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.691][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:03.692][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:03.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.694][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.695][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.702][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:03.703][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:03.704][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.705][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:03.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:03.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:03.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:03.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:03.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:03.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:03.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:03.749][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-04-12 04:59:03.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:03.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:03.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:03.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:03.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:03.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:03.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:03.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:03.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:03.773][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-04-12 04:59:03.774][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:03.776][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-04-12 04:59:03.777][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:03.778][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:03.779][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:03.780][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:03.781][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:03.782][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:03.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:03.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:03.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:03.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:03.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:03.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:03.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:03.796][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-04-12 04:59:03.798][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:03.799][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:03.801][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-04-12 04:59:04.251][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-04-12 04:59:04.713][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:04.720][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-04-12 04:59:04.741][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-04-12 04:59:04.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-04-12 04:59:04.756][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:04.774][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:04.775][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:04.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:04.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:04.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:04.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:04.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:04.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:04.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:04.789][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.790][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.792][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.800][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:04.801][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:04.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.802][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.804][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:04.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:04.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.810][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:04.811][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:04.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.813][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:04.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:04.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.821][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:04.822][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:04.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.823][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.825][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:04.826][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:04.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.827][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.829][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:04.830][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:04.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.831][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.833][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:04.834][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.835][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.843][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:04.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:04.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.846][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:04.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:04.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.858][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:04.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:04.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.862][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:04.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.875][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:04.876][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:04.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.879][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:04.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.891][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:04.893][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:04.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.896][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:04.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:04.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:04.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:04.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:04.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:04.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:04.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:04.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:04.962][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-04-12 04:59:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:04.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:04.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:04.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:04.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:04.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:04.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:04.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:04.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:04.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:04.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:04.985][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-04-12 04:59:04.986][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:04.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-04-12 04:59:04.989][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:04.990][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:04.991][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:04.992][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:04.993][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:04.994][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:04.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:04.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:04.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:05.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:05.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:05.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:05.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:05.007][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-04-12 04:59:05.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:05.011][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:05.012][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-04-12 04:59:05.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-04-12 04:59:06.137][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:06.148][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-04-12 04:59:06.176][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-04-12 04:59:06.194][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-04-12 04:59:06.199][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:06.230][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:06.232][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:06.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:06.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:06.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:06.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:06.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:06.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:06.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:06.283][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.285][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.287][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.288][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.300][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:06.302][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:06.303][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.305][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:06.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:06.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.315][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:06.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:06.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.318][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.319][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:06.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:06.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.327][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:06.328][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:06.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:06.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:06.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.338][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:06.339][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:06.340][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.341][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:06.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:06.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.349][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:06.350][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:06.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.352][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.354][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:06.355][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.356][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.357][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.358][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:06.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:06.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.368][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:06.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:06.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.377][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:06.379][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:06.380][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.381][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:06.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:06.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.391][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:06.393][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:06.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.396][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:06.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:06.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.404][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:06.406][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:06.407][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.408][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:06.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:06.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:06.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:06.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:06.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:06.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:06.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:06.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:06.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:06.460][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-04-12 04:59:06.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:06.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:06.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:06.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:06.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:06.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:06.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:06.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:06.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:06.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:06.490][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-04-12 04:59:06.491][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:06.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-04-12 04:59:06.494][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:06.495][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:06.496][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:06.497][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:06.498][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:06.499][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:06.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:06.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:06.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:06.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:06.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:06.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:06.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:06.514][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-04-12 04:59:06.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:06.518][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:06.519][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-04-12 04:59:06.988][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-04-12 04:59:07.459][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-04-12 04:59:07.466][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-04-12 04:59:07.473][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-04-12 04:59:07.491][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-04-12 04:59:07.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-04-12 04:59:07.511][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:07.533][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:07.535][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:07.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:07.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:07.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:07.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:07.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:07.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:07.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:07.548][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.549][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.550][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.551][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.567][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:07.568][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:07.569][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.570][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.571][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:07.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:07.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.578][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:07.579][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:07.580][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.581][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:07.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.588][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:07.589][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:07.590][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.591][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:07.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:07.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.599][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:07.600][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:07.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.602][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:07.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:07.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.610][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:07.611][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:07.612][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.612][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.614][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:07.615][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.616][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.618][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:07.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.624][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:07.625][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:07.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.627][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:07.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:07.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.634][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:07.635][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:07.636][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.637][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:07.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:07.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.645][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:07.646][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:07.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.648][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.650][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:07.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:07.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.657][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:07.658][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:07.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.660][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.662][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:07.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:07.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:07.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:07.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:07.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:07.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:07.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:07.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:07.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:07.711][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-04-12 04:59:07.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:07.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:07.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:07.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:07.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:07.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:07.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:07.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:07.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:07.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:07.742][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-04-12 04:59:07.743][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:07.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-04-12 04:59:07.746][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:07.747][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:07.748][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:07.749][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:07.750][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:07.750][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:07.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:07.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:07.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:07.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:07.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:07.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:07.762][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[2023-04-12 04:59:07.764][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-04-12 04:59:07.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:07.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:07.768][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-04-12 04:59:09.333][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-04-12 04:59:09.858][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:09.866][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-04-12 04:59:09.878][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-04-12 04:59:09.888][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-04-12 04:59:09.893][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:09.911][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:09.913][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:09.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:09.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:09.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:09.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:09.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:09.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:09.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:09.926][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:09.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:09.928][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.929][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:09.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:09.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.936][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:09.937][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:09.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.939][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.940][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:09.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:09.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.947][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:09.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:09.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.950][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.951][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:09.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:09.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.965][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:09.966][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:09.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.968][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:09.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:09.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.976][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:09.977][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:09.978][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.979][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:09.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:09.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.986][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:09.987][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:09.988][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.989][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.990][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:09.991][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:09.992][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.993][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:09.994][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:09.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:09.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:09.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.000][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:10.001][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:10.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.003][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:10.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:10.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.011][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:10.012][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:10.013][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.014][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:10.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:10.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.021][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:10.022][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:10.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.024][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.025][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:10.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:10.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.032][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:10.033][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:10.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.034][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:10.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:10.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:10.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:10.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:10.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:10.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:10.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:10.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:10.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:10.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:10.082][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-04-12 04:59:10.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:10.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:10.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:10.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:10.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:10.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:10.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:10.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:10.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:10.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:10.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:10.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:10.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:10.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:10.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:10.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:10.104][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-04-12 04:59:10.105][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:10.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-04-12 04:59:10.108][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:10.109][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:10.110][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:10.111][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:10.112][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:10.112][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:10.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:10.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:10.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:10.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:10.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:10.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:10.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:10.131][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-04-12 04:59:10.134][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:10.134][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:10.136][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-04-12 04:59:10.602][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-04-12 04:59:11.151][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:11.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-04-12 04:59:11.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-04-12 04:59:11.181][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-04-12 04:59:11.185][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:11.202][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:11.204][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:11.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:11.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:11.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:11.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:11.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:11.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:11.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:11.218][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.219][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.220][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.220][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.228][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:11.229][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:11.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.231][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.232][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:11.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:11.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.239][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:11.240][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:11.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.242][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.243][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:11.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:11.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.250][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:11.251][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:11.252][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.253][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:11.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:11.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.261][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:11.262][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:11.263][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.264][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:11.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:11.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.281][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:11.283][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:11.285][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.286][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.288][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:11.289][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.291][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.292][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.294][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:11.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:11.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:11.307][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.308][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:11.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:11.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.319][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:11.321][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:11.322][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.324][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:11.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:11.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.340][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:11.341][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:11.342][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.344][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:11.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:11.351][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:11.352][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.353][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:11.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:11.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:11.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:11.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:11.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:11.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:11.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:11.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:11.401][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-04-12 04:59:11.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:11.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:11.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:11.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:11.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:11.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:11.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:11.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:11.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:11.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:11.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:11.425][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-04-12 04:59:11.426][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:11.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-04-12 04:59:11.428][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:11.429][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:11.430][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:11.431][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:11.432][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:11.433][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:11.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:11.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:11.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:11.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:11.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:11.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:11.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:11.447][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-04-12 04:59:11.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:11.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:11.452][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-04-12 04:59:11.912][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-04-12 04:59:12.381][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:12.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-04-12 04:59:12.414][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-04-12 04:59:12.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-04-12 04:59:12.436][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:12.468][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:12.470][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:12.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:12.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:12.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:12.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:12.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:12.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:12.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:12.487][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.489][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.498][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:12.499][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:12.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.501][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.503][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:12.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:12.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.510][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:12.511][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:12.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.513][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.514][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:12.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:12.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.522][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:12.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:12.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.525][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:12.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:12.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.533][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:12.534][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:12.535][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.536][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:12.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:12.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.544][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:12.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:12.546][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.547][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.549][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:12.550][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.550][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.551][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.553][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:12.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.575][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:12.576][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:12.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.579][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:12.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.588][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:12.589][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:12.590][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.591][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:12.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:12.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.599][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:12.600][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:12.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.602][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.603][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:12.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:12.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:12.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:12.612][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.613][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.614][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:12.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:12.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:12.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:12.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:12.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:12.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:12.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:12.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:12.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:12.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:12.664][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-04-12 04:59:12.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:12.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:12.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:12.714][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 [2023-04-12 04:59:12.717][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2023-04-12 04:59:12.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:12.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:12.722][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:13.305][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:13.939][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:13.951][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-04-12 04:59:13.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-04-12 04:59:14.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.073][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.TRACE[2023-04-12 04:59:14.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.124][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[2023-04-12 04:59:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.268][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[2023-04-12 04:59:14.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.388][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.TRACE[2023-04-12 04:59:14.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:14.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:14.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:14.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:14.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:14.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:14.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:14.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:14.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:14.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:14.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:14.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:14.640][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:14.644][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:14.645][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:14.647][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:15.156][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:15.705][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:15.713][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-04-12 04:59:15.726][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-04-12 04:59:15.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:15.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:15.750][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:15.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:16.198][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:16.648][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:16.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-04-12 04:59:16.678][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-04-12 04:59:16.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:16.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:16.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:16.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:16.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:16.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:16.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:16.708][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-04-12 04:59:16.709][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:16.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-04-12 04:59:16.717][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:16.719][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:16.721][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:16.722][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:16.723][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:16.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:16.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:16.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:16.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:16.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:16.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:16.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:16.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:16.741][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-04-12 04:59:16.744][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:16.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:16.747][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-04-12 04:59:17.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-04-12 04:59:17.646][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:17.653][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-04-12 04:59:17.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-04-12 04:59:17.687][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-04-12 04:59:17.692][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:17.710][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:17.712][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:17.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:17.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:17.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:17.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:17.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:17.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:17.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:17.727][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.729][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.738][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:17.739][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:17.740][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.741][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.742][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:17.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.749][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:17.750][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:17.751][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.752][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:17.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:17.761][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:17.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.763][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:17.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:17.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:17.772][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:17.773][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.774][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:17.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:17.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.782][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:17.783][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:17.784][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.785][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.787][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:17.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:17.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.793][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:17.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:17.795][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.796][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.797][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:17.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.804][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.807][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.815][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:17.817][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:17.817][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.818][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:17.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:17.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.827][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:17.828][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:17.829][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.829][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.831][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:17.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:17.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.837][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:17.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:17.839][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.840][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:17.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:17.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:17.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:17.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:17.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:17.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:17.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:17.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:17.899][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-04-12 04:59:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:17.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:17.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:17.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:17.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:17.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:17.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:17.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:17.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:17.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:17.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:17.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:17.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:17.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:17.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:17.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:17.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:17.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:17.946][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-04-12 04:59:17.947][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:17.949][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-04-12 04:59:17.950][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:17.951][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:17.952][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:17.953][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:17.954][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:17.955][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:17.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:17.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:17.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:17.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:17.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:17.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:17.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:17.968][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-04-12 04:59:17.971][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:17.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:17.973][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-04-12 04:59:18.415][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-04-12 04:59:21.895][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:21.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-04-12 04:59:21.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-04-12 04:59:21.957][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-04-12 04:59:21.963][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:21.994][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:21.996][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:21.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.019][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.021][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.022][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.024][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.038][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:22.039][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:22.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.042][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.044][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:22.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:22.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.050][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:22.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:22.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.053][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:22.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:22.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:22.062][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:22.063][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.064][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:22.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:22.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:22.072][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:22.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.074][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:22.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:22.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:22.082][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:22.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.084][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.085][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:22.086][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:22.087][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.088][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.089][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:22.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:22.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.096][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.097][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.098][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.099][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.106][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:22.107][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:22.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.109][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:22.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.117][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:22.118][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:22.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.120][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.121][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:22.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:22.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.127][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:22.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:22.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.130][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:22.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:22.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:22.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:22.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:22.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:22.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:22.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:22.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:22.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.183][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-04-12 04:59:22.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.232][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:22.236][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:22.237][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-12 04:59:22.238][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:22.239][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-12 04:59:22.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.407][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[2023-04-12 04:59:22.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.604][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[2023-04-12 04:59:22.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.675][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.TRACE[2023-04-12 04:59:22.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.700][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.TRACE[2023-04-12 04:59:22.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.779][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:22.783][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:22.784][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-12 04:59:22.786][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:22.787][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-12 04:59:22.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.876][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.TRACE[2023-04-12 04:59:22.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:22.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:22.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:22.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:22.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:22.982][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.TRACE[2023-04-12 04:59:22.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:22.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:22.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:22.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:22.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:22.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:22.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.055][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.TRACE[2023-04-12 04:59:23.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.077][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.TRACE[2023-04-12 04:59:23.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:23.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:23.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.265][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:23.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:23.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:23.280][biodb::testThat]
biodb.INFO [2023-04-12 04:59:23.281][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-12 04:59:23.282][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:23.283][biodb::testThat]
biodb.TRACE[2023-04-12 04:59:23.286][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:59:23.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:59:23.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:23.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:23.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:23.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:23.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:23.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:23.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:23.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:23.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:23.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:23.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:23.366][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:23.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:23.371][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:23.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:23.815][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:24.261][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:24.269][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-04-12 04:59:24.281][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-04-12 04:59:24.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:24.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:24.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:24.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:24.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:24.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:24.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:24.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:24.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:24.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:24.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:24.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:24.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:24.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:24.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:24.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:24.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:24.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:24.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:24.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:24.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:24.318][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:24.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:25.318][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:25.329][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-04-12 04:59:25.346][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-04-12 04:59:25.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:25.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:25.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:25.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:25.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:25.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:25.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:25.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:25.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:25.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:25.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:25.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:25.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:25.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:25.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:25.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:25.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:25.392][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:25.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:25.396][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:25.398][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:25.859][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:26.464][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:26.470][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-04-12 04:59:26.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-04-12 04:59:26.487][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:26.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:26.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:26.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:26.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:26.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:26.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:26.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:26.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.507][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.508][private$selectFields]
biodb.TRACE[2023-04-12 04:59:26.509][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:26.510][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:26.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.514][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.514][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.515][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.516][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.518][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.520][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.522][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.533][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.535][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:26.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.558][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-12 04:59:26.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:26.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:26.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:26.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:26.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:26.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:26.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:26.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.580][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.581][private$selectFields]
biodb.TRACE[2023-04-12 04:59:26.582][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:26.583][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:26.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.588][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.589][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.590][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.592][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.593][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.594][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:26.595][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.596][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.598][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.599][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:26.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.613][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-12 04:59:26.614][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:26.614][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:26.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:26.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:26.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:26.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:26.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:26.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:26.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:26.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:26.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:26.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:26.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:26.765][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:26.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:26.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:26.772][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:27.239][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:27.755][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:27.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-04-12 04:59:27.776][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-04-12 04:59:27.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:27.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:27.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:27.790][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:28.268][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:28.743][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:28.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-04-12 04:59:28.765][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-04-12 04:59:28.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:28.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:28.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:28.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:28.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:28.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:28.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:28.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:28.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:28.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:28.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:28.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:28.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:28.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:28.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:28.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:28.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:28.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:28.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:28.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:28.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:28.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:28.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:28.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:28.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:28.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:28.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:28.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:28.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:28.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:28.867][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:29.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.118][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.119][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.120][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.121][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.125][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.125][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.128][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.129][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.130][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.131][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.135][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.136][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.149][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-12 04:59:29.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.200][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.201][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.202][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.203][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.204][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.208][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.211][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.212][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.213][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.238][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.239][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.255][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-12 04:59:29.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.280][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.281][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.282][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.288][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.289][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.290][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.291][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.292][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.293][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.294][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.295][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.296][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.297][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.300][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.301][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.316][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-12 04:59:29.317][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:29.318][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:29.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:29.334][biodb::testThat]
biodb.INFO [2023-04-12 04:59:29.335][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-12 04:59:29.336][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:29.337][biodb::testThat]
biodb.TRACE[2023-04-12 04:59:29.342][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:59:29.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:59:29.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:29.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:29.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:29.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-12 04:59:29.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:29.455][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-12 04:59:29.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:29.487][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:29.489][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-12 04:59:29.490][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:29.491][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-12 04:59:29.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.519][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:29.522][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:29.523][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-12 04:59:29.525][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:29.526][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-12 04:59:29.529][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:29.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.541][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.TRACE[2023-04-12 04:59:29.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.550][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.551][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.552][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.553][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.555][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.556][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.557][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.559][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.561][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.563][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.564][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.565][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.566][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.567][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.569][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.570][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.583][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-12 04:59:29.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.603][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.604][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.605][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.606][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.608][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.609][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.610][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.614][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.616][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.620][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.621][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.634][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-12 04:59:29.635][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:29.636][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:29.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:29.721][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:29.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:29.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-04-12 04:59:29.728][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:29.730][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-04-12 04:59:29.733][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:29.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:29.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-04-12 04:59:29.739][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:29.740][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-04-12 04:59:29.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:29.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:29.819][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:29.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.841][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.842][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.843][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.847][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.848][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.849][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.850][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.851][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.853][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.854][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.855][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.856][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.856][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.857][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.870][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-12 04:59:29.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.890][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.891][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.892][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.892][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.893][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.895][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.896][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.897][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.899][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.900][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.901][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.903][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.905][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.907][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.908][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.920][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-12 04:59:29.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:29.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:29.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:29.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:29.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:29.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:29.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:29.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.942][private$selectFields]
biodb.TRACE[2023-04-12 04:59:29.943][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:29.944][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:29.945][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.948][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.950][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.953][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.954][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:29.955][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.956][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.958][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.959][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:29.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:29.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.972][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-12 04:59:29.973][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:29.974][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:29.982][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:29.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:29.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:29.987][biodb::testThat]
biodb.INFO [2023-04-12 04:59:29.988][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-12 04:59:29.989][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:29.990][biodb::testThat]
biodb.TRACE[2023-04-12 04:59:29.994][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:59:29.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:59:29.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:29.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:29.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:29.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:30.077][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:30.080][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:30.082][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-12 04:59:30.083][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:30.084][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-12 04:59:30.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:30.112][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:30.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-12 04:59:30.115][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:30.116][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-12 04:59:30.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:30.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.141][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:30.144][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:30.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-12 04:59:30.146][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:30.148][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-12 04:59:30.150][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:30.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.170][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.171][private$selectFields]
biodb.TRACE[2023-04-12 04:59:30.172][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:30.173][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:30.173][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.174][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.176][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.177][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.180][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.181][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.182][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.183][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.186][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.187][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.188][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:30.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.201][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-12 04:59:30.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.221][private$selectFields]
biodb.TRACE[2023-04-12 04:59:30.222][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:30.223][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:30.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.228][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.231][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.232][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.233][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.234][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.235][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.238][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.239][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:30.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.252][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-12 04:59:30.253][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:30.254][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:30.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.310][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[2023-04-12 04:59:30.351][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:30.361][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:30.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-04-12 04:59:30.364][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:30.365][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-04-12 04:59:30.369][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:30.372][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:30.373][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-04-12 04:59:30.374][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:30.376][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-04-12 04:59:30.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.388][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.TRACE[2023-04-12 04:59:30.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.432][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.TRACE[2023-04-12 04:59:30.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:30.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:30.445][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:30.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.465][private$selectFields]
biodb.TRACE[2023-04-12 04:59:30.466][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:30.467][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:30.468][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.474][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.477][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.480][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.481][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.484][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.489][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.490][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:30.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.511][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-12 04:59:30.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:30.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.542][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.543][private$selectFields]
biodb.TRACE[2023-04-12 04:59:30.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:30.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:30.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.552][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.554][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.556][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.558][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.560][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.563][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.565][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.567][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.569][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.571][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:30.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.591][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-12 04:59:30.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.609][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.TRACE[2023-04-12 04:59:30.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.624][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.626][private$selectFields]
biodb.TRACE[2023-04-12 04:59:30.628][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:30.629][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:30.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.635][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.636][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.637][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.641][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.643][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-12 04:59:30.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.645][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.647][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.648][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-12 04:59:30.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:30.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:30.660][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-12 04:59:30.661][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:30.662][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:30.683][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:30.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:30.688][biodb::testThat]
biodb.INFO [2023-04-12 04:59:30.689][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-12 04:59:30.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:30.691][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:30.693][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-12 04:59:30.694][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:30.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-12 04:59:30.697][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:30.698][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:30.699][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:30.700][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:30.701][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:30.702][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:30.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:30.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:30.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:30.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:30.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:30.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:30.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:30.720][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-04-12 04:59:30.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:30.724][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:30.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-04-12 04:59:31.208][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-04-12 04:59:31.651][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:31.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-04-12 04:59:31.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-04-12 04:59:31.695][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-04-12 04:59:31.701][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:31.720][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:31.722][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:31.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:31.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:31.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:31.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:31.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:31.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:31.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:31.737][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.739][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.740][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.748][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:31.750][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:31.751][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.752][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.754][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:31.756][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:31.757][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.759][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.761][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:31.763][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:31.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.765][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.767][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:31.769][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:31.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.774][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:31.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:31.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.779][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.781][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:31.782][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:31.784][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.785][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.787][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:31.789][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:31.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.792][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.794][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:31.795][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:31.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.798][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.800][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:31.802][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:31.803][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.805][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.807][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:31.808][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:31.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.811][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:31.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:31.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:31.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:31.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:31.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:31.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:31.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:31.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:31.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:31.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:31.879][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-04-12 04:59:31.881][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-12 04:59:31.891][biodb::testThat]
biodb.INFO [2023-04-12 04:59:31.893][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-12 04:59:31.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:31.897][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:31.911][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-04-12 04:59:31.913][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-04-12 04:59:31.915][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-04-12 04:59:31.918][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-04-12 04:59:31.920][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-04-12 04:59:31.922][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:31.924][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:31.925][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:31.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:31.928][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:31.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:31.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:31.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:31.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:31.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:31.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:31.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:31.953][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-04-12 04:59:31.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:31.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:31.961][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-04-12 04:59:32.409][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-04-12 04:59:32.867][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:32.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-04-12 04:59:32.920][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-04-12 04:59:32.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:32.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:32.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:32.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:32.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:32.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:32.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:32.947][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-04-12 04:59:32.951][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:32.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:32.955][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-04-12 04:59:33.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-04-12 04:59:33.868][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:33.880][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-04-12 04:59:33.899][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-04-12 04:59:33.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:33.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:33.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:33.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:33.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:33.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:33.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:33.923][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-04-12 04:59:33.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:33.929][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:33.931][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-04-12 04:59:34.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-04-12 04:59:34.847][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:34.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-04-12 04:59:34.874][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-04-12 04:59:34.889][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-04-12 04:59:34.894][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:34.918][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-04-12 04:59:34.920][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:34.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:34.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:34.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:34.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:34.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:34.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:34.935][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[2023-04-12 04:59:34.938][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:34.940][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:34.941][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.942][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:34.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:34.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.952][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:34.953][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:34.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.955][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.956][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:34.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:34.958][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.959][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.961][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:34.962][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:34.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.964][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.965][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:34.967][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:34.968][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.969][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:34.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:34.972][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.973][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.975][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:34.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:34.977][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.978][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.979][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:34.980][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:34.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.982][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.984][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:34.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:34.986][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.987][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.988][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:34.990][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:34.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.992][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.993][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:34.994][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:34.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:34.996][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:34.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:34.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:35.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:35.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:35.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:35.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:35.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:35.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:35.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:35.062][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.066][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.075][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:35.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:35.078][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.079][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.081][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:35.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.088][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:35.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:35.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.091][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:35.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:35.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:35.102][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:35.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.104][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:35.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:35.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.117][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.127][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.130][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.131][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.139][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:35.140][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:35.141][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.142][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.144][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:35.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:35.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.151][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.153][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.154][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.162][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:35.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:35.165][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.165][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:35.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:35.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.174][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:35.175][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:35.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.177][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.179][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:35.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:35.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:35.188][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:35.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.190][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.192][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:35.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:35.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:35.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:35.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:35.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:35.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:35.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:35.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:35.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:35.246][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.249][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.258][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:35.260][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:35.261][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.261][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.263][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:35.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:35.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.272][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:35.273][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:35.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.275][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:35.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:35.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:35.285][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:35.286][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.287][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:35.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:35.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.297][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.298][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.300][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:35.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.311][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.312][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.313][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.314][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:35.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.325][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:35.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:35.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.329][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.330][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:35.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.339][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:35.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.352][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:35.354][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:35.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.356][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:35.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:35.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:35.367][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:35.368][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.369][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:35.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.380][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:35.381][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:35.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.383][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.385][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:35.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:35.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:35.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:35.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:35.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:35.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:35.503][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-04-12 04:59:35.505][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-12 04:59:35.506][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-12 04:59:35.521][biodb::testThat]
biodb.INFO [2023-04-12 04:59:35.523][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-12 04:59:35.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:35.525][biodb::testThat]
biodb.INFO [2023-04-12 04:59:35.552][biodb::testThat]
biodb.INFO [2023-04-12 04:59:35.553][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-12 04:59:35.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:35.556][biodb::testThat]
biodb.INFO [2023-04-12 04:59:35.564][biodb::testThat]
biodb.INFO [2023-04-12 04:59:35.565][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-12 04:59:35.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:35.567][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:35.570][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:35.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:35.575][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:35.577][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:36.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:37.039][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:37.047][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-04-12 04:59:37.060][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-04-12 04:59:37.078][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:37.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:37.080][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:37.081][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:37.082][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:37.083][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:37.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:37.085][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:37.087][biodb::testThat]
biodb.INFO [2023-04-12 04:59:37.088][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-12 04:59:37.089][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:37.089][biodb::testThat]
biodb.ERROR[2023-04-12 04:59:37.105][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-12 04:59:37.123][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-12 04:59:37.135][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:59:37.136][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-12 04:59:37.138][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-12 04:59:37.139][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:59:37.140][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.141][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.143][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:59:37.155][biodb::testContext]
biodb.INFO [2023-04-12 04:59:37.156][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:59:37.157][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-04-12 04:59:37.158][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:59:37.159][biodb::testContext]
biodb.INFO [2023-04-12 04:59:37.164][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:59:37.166][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:59:37.170][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:37.171][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:59:37.172][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:59:37.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.176][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:59:37.177][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:59:37.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.181][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:59:37.182][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:59:37.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.185][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[2023-04-12 04:59:37.186][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:59:37.187][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:59:37.188][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:59:37.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.200][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:59:37.202][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:59:37.203][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:59:37.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.206][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:59:37.207][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:59:37.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.211][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:59:37.212][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:59:37.214][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:59:37.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.219][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:59:37.221][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:59:37.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.226][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:59:37.227][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:59:37.229][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:59:37.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.234][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:59:37.236][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:59:37.237][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:59:37.239][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:59:37.240][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:59:37.242][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:59:37.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.247][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:59:37.249][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:59:37.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.253][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[2023-04-12 04:59:37.254][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:59:37.256][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:59:37.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.261][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:59:37.263][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:59:37.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.268][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:59:37.270][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:59:37.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.275][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:59:37.277][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:59:37.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.281][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[2023-04-12 04:59:37.282][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:59:37.284][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:59:37.289][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:59:37.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.297][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:59:37.299][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:59:37.300][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:59:37.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.303][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[2023-04-12 04:59:37.304][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:59:37.306][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.321][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:59:37.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:37.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.326][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.328][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:59:37.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:37.330][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.331][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:59:37.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:37.333][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.334][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.335][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:37.335][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:37.335][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:37.335][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:59:37.335][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:59:37.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:37.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:37.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.341][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.342][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.343][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:37.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:37.345][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.346][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.347][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:59:37.349][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.350][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:59:37.351][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:37.352][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.353][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.354][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.355][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.356][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:59:37.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:37.358][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.359][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:59:37.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:37.361][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.362][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.363][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:37.363][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:37.363][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:37.363][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:59:37.363][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:59:37.364][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:37.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:37.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.370][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:37.372][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:37.373][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.374][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.375][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:59:37.377][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.378][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:59:37.379][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.380][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:37.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.381][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.382][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.383][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.384][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:59:37.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:37.386][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.387][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:59:37.388][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:37.389][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.390][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.391][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.392][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:37.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.395][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:37.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.398][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.399][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.400][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:37.401][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:37.402][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.403][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.404][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:59:37.406][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.407][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:59:37.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:37.410][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.411][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.413][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.414][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:59:37.415][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:37.416][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.417][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:59:37.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:37.419][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.420][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.421][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.422][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:37.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.425][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:37.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.428][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.429][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:37.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:37.432][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.433][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:37.435][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:37.436][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.441][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[2023-04-12 04:59:37.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.459][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[2023-04-12 04:59:37.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.468][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[2023-04-12 04:59:37.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.472][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[2023-04-12 04:59:37.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.481][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[2023-04-12 04:59:37.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.513][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:59:37.521][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:59:37.522][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:59:37.524][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:59:37.525][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:59:37.527][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:59:37.528][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:59:37.529][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:59:37.530][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:59:37.532][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:59:37.533][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:59:37.534][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:59:37.536][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:59:37.537][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:59:37.538][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:59:37.540][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:59:37.541][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:59:37.542][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:59:37.543][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:59:37.545][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:59:37.546][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:59:37.547][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:59:37.549][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:59:37.550][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:59:37.551][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:59:37.553][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:59:37.554][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:59:37.555][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:59:37.556][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:59:37.558][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:59:37.559][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:59:37.560][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:59:37.561][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:59:37.563][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:59:37.564][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:59:37.565][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:59:37.566][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:59:37.568][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:59:37.569][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:59:37.570][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:59:37.572][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:59:37.573][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:59:37.574][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:59:37.575][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:59:37.577][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:59:37.578][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:59:37.579][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:59:37.581][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:59:37.582][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:59:37.583][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:59:37.584][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:59:37.585][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:59:37.587][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:59:37.588][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:59:37.589][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:59:37.590][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:59:37.592][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:59:37.593][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:59:37.594][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:59:37.596][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:59:37.597][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:59:37.598][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:59:37.599][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:59:37.601][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:59:37.602][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:59:37.603][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:59:37.604][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:59:37.606][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:59:37.607][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:59:37.608][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:59:37.609][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:59:37.611][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:59:37.612][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:59:37.613][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:59:37.614][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:59:37.616][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:59:37.617][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:59:37.618][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:59:37.620][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:59:37.621][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:59:37.622][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:59:37.623][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:59:37.625][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:59:37.626][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:59:37.628][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:59:37.629][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:37.629][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.631][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.642][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[2023-04-12 04:59:37.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.648][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[2023-04-12 04:59:37.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.726][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[2023-04-12 04:59:37.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:37.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:37.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:37.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:37.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:37.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:37.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:37.741][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-12 04:59:37.742][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-12 04:59:37.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.745][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:37.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.751][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.752][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-12 04:59:37.753][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:59:37.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:37.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.756][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-12 04:59:37.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-12 04:59:37.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-12 04:59:37.759][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:37.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:37.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:37.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:37.761][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:59:37.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:37.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:37.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:37.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:37.768][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:37.768][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-12 04:59:37.769][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:37.770][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:37.771][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:37.772][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-12 04:59:37.772][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-12 04:59:37.773][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:59:37.775][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:59:37.777][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-12 04:59:37.779][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:59:37.781][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:59:37.782][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:59:37.786][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-12 04:59:37.787][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-12 04:59:37.789][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-12 04:59:37.790][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-12 04:59:37.792][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:59:37.793][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:59:37.794][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-12 04:59:37.795][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-12 04:59:37.797][biodb::testThat]
biodb.INFO [2023-04-12 04:59:37.798][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-04-12 04:59:37.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:37.809][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:37.813][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-12 04:59:37.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:37.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:37.819][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-04-12 04:59:38.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-04-12 04:59:38.870][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:38.878][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-04-12 04:59:38.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-04-12 04:59:38.895][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:38.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:38.900][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:38.901][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:39.343][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:39.798][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:39.805][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-04-12 04:59:39.816][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-04-12 04:59:39.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:39.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:39.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:39.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:39.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:39.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:39.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:39.848][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:39.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:39.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:39.871][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:40.300][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:40.756][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:40.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-04-12 04:59:40.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-04-12 04:59:40.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.829][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:40.832][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:40.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-04-12 04:59:40.835][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:40.836][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-04-12 04:59:40.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.847][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[2023-04-12 04:59:40.849][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:40.852][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:40.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-04-12 04:59:40.854][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:40.856][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-04-12 04:59:40.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.881][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:40.884][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:40.885][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-04-12 04:59:40.887][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:40.888][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-04-12 04:59:40.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.901][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:40.904][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:40.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-04-12 04:59:40.907][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:40.908][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-04-12 04:59:40.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.921][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:40.924][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:40.925][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:40.927][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:42.419][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:42.875][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:42.886][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-04-12 04:59:42.904][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-04-12 04:59:42.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:42.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:42.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:42.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:42.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:42.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:42.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:59:42.932][biodb::testThat]
biodb.INFO [2023-04-12 04:59:42.933][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-04-12 04:59:42.935][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:42.936][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:42.942][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:42.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:42.949][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:42.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:43.462][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:43.925][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:43.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-04-12 04:59:43.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-04-12 04:59:43.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:43.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:43.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:43.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:43.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:43.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:43.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:43.961][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:43.964][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:43.965][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:43.967][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-12 04:59:44.407][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:44.973][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:44.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-04-12 04:59:45.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-04-12 04:59:45.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:45.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:59:45.027][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:59:45.029][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-12 04:59:45.030][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-12 04:59:45.032][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:59:45.033][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.035][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.038][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:59:45.044][biodb::testContext]
biodb.INFO [2023-04-12 04:59:45.046][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:59:45.047][biodb::testContext] Test context - Test web services
biodb.INFO [2023-04-12 04:59:45.048][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:59:45.050][biodb::testContext]
biodb.INFO [2023-04-12 04:59:45.057][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:59:45.059][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:59:45.065][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:45.067][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:59:45.068][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:59:45.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.073][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[2023-04-12 04:59:45.075][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:59:45.077][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:59:45.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.083][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:59:45.084][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:59:45.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.089][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:59:45.090][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:59:45.091][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:59:45.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.094][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:59:45.095][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:59:45.096][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:59:45.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.099][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:59:45.100][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:59:45.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.104][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:59:45.105][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:59:45.106][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:59:45.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.109][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:59:45.110][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:59:45.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.114][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:59:45.114][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:59:45.116][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:59:45.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.119][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:59:45.120][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:59:45.121][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:59:45.122][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:59:45.123][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:59:45.124][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:59:45.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.127][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:59:45.128][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:59:45.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.132][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:59:45.133][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:59:45.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.136][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:59:45.137][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:59:45.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.140][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:59:45.141][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:59:45.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.145][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:59:45.146][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:59:45.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.149][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:59:45.150][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:59:45.155][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:59:45.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.159][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:59:45.160][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:59:45.161][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:59:45.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.165][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:59:45.166][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.168][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:59:45.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:45.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.172][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.173][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.174][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.175][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:59:45.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:45.177][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.178][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:59:45.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:45.180][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.181][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.182][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:45.182][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:45.182][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:45.182][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:59:45.182][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:59:45.183][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:45.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.185][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:45.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.188][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.189][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.190][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:45.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:45.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.193][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.194][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:59:45.195][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.196][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:59:45.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:45.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.201][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:59:45.204][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:45.205][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.206][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:59:45.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:45.208][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.209][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.210][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:45.210][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:45.210][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:45.210][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:59:45.210][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:59:45.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:45.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.214][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:45.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.217][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.218][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.219][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:45.220][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:45.221][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.222][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.223][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:59:45.225][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.226][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:59:45.227][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.228][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:45.228][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.229][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.230][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.231][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.232][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:59:45.233][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:45.234][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.235][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:59:45.236][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:45.237][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.238][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.239][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:45.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.242][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:45.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.245][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.246][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.247][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:45.248][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:45.249][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.249][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.250][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:59:45.252][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.253][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:59:45.254][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.255][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:45.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.258][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.259][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.259][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:59:45.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:45.261][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.262][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:59:45.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:45.264][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.265][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.266][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.271][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:45.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.277][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:45.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.280][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.281][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.282][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:45.282][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:45.283][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.284][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:45.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:45.286][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.295][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[2023-04-12 04:59:45.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.303][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[2023-04-12 04:59:45.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.315][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[2023-04-12 04:59:45.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.343][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[2023-04-12 04:59:45.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.356][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:59:45.357][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:59:45.358][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:59:45.359][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:59:45.361][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:59:45.362][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:59:45.363][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:59:45.364][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:59:45.366][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:59:45.367][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:59:45.368][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:59:45.369][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:59:45.370][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:59:45.372][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:59:45.373][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:59:45.374][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:59:45.375][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:59:45.377][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:59:45.378][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:59:45.379][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:59:45.380][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:59:45.382][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:59:45.383][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:59:45.384][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:59:45.385][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:59:45.387][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:59:45.388][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:59:45.389][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:59:45.390][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:59:45.392][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:59:45.393][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:59:45.394][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:59:45.396][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:59:45.397][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:59:45.398][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:59:45.399][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:59:45.401][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:59:45.402][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:59:45.403][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:59:45.404][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:59:45.406][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:59:45.407][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:59:45.408][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:59:45.409][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:59:45.411][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:59:45.412][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:59:45.413][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:59:45.414][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:59:45.416][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:59:45.417][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:59:45.418][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:59:45.419][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:59:45.421][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:59:45.422][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:59:45.423][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:59:45.424][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:59:45.426][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:59:45.427][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:59:45.428][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:59:45.429][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:59:45.431][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:59:45.432][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:59:45.433][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:59:45.434][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:59:45.436][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:59:45.437][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:59:45.438][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:59:45.440][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:59:45.441][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:59:45.442][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:59:45.443][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:59:45.445][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:59:45.446][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:59:45.447][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:59:45.448][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:59:45.450][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:59:45.451][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:59:45.452][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:59:45.453][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:59:45.455][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:59:45.456][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:59:45.457][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:59:45.458][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:59:45.460][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:59:45.461][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:59:45.462][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:45.463][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.465][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:45.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:45.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:45.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:45.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:45.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:45.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:45.569][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-12 04:59:45.570][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-12 04:59:45.572][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.573][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.574][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.575][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:45.576][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.577][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.577][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.578][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-12 04:59:45.579][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:59:45.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:45.581][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.582][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-12 04:59:45.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-12 04:59:45.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-12 04:59:45.585][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:45.586][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:45.586][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:45.586][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:45.587][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:59:45.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.589][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:45.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:45.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:45.592][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:45.593][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:45.593][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-12 04:59:45.594][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:45.595][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:45.595][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:45.596][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-12 04:59:45.596][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-12 04:59:45.598][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:59:45.599][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:59:45.601][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-12 04:59:45.602][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:59:45.603][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:59:45.605][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:59:45.608][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-12 04:59:45.609][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-12 04:59:45.610][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-12 04:59:45.611][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-12 04:59:45.612][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:59:45.613][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:59:45.614][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-12 04:59:45.615][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-12 04:59:45.616][biodb::testThat]
biodb.INFO [2023-04-12 04:59:45.617][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-04-12 04:59:45.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:45.619][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:45.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-12 04:59:45.625][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:45.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-12 04:59:45.628][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:45.629][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-12 04:59:45.633][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:45.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:45.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:45.639][private$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[2023-04-12 04:59:46.096][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-12 04:59:46.560][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:46.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-04-12 04:59:46.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-04-12 04:59:46.599][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:59:46.601][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-12 04:59:46.603][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-12 04:59:46.604][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:59:46.606][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:46.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:46.608][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.611][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:59:46.618][biodb::testContext]
biodb.INFO [2023-04-12 04:59:46.619][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:59:46.620][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-04-12 04:59:46.622][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:59:46.623][biodb::testContext]
biodb.INFO [2023-04-12 04:59:46.630][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:59:46.633][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:59:46.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:46.640][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:59:46.641][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:59:46.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.647][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:59:46.648][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:59:46.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.653][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:59:46.655][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:59:46.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.660][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:59:46.661][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:59:46.662][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:59:46.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.667][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:59:46.669][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:59:46.670][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:59:46.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.676][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:59:46.679][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:59:46.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.687][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:59:46.689][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:59:46.691][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:59:46.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.695][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:59:46.696][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:59:46.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.700][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:59:46.701][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:59:46.702][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:59:46.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.706][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:59:46.707][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:59:46.708][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:59:46.709][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:59:46.710][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:59:46.711][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:59:46.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.713][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[2023-04-12 04:59:46.714][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:59:46.715][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:59:46.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.719][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:59:46.720][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:59:46.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.723][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:59:46.724][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:59:46.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:59:46.729][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:59:46.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.733][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:59:46.734][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:59:46.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.737][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:59:46.738][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:59:46.743][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:59:46.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.746][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[2023-04-12 04:59:46.747][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:59:46.748][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:59:46.760][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:59:46.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.764][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:59:46.766][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.767][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:59:46.768][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.769][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:46.770][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.771][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.772][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.773][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.774][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:59:46.775][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:46.776][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.777][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:59:46.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:46.779][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:46.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:46.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:46.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:59:46.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:59:46.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:46.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:46.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.788][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.789][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:46.790][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:46.791][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.792][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.793][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:59:46.794][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.795][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:59:46.796][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.797][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:46.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.800][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.801][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.802][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:59:46.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:46.804][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.805][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:59:46.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:46.806][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.807][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.808][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:46.808][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:46.808][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:46.808][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:59:46.808][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:59:46.809][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:46.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.812][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:46.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.815][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.816][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.817][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:46.817][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:46.818][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.819][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.820][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:59:46.822][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.823][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:59:46.824][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:46.826][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.827][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.828][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.829][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.829][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:59:46.830][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:46.831][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.832][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:59:46.833][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:46.834][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.835][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.836][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.837][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:46.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.839][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:46.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.843][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:46.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:46.845][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.846][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.847][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:59:46.849][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.850][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:59:46.851][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.852][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:46.853][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.854][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.855][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.857][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:59:46.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:46.859][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.860][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:59:46.861][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:46.862][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.863][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:46.864][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.865][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:59:46.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.866][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.867][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:46.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:46.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:46.870][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:46.871][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.872][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:46.873][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:46.874][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:46.875][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:59:46.877][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:46.877][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.883][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[2023-04-12 04:59:46.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.896][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[2023-04-12 04:59:46.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.914][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[2023-04-12 04:59:46.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.935][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.DEBUG[2023-04-12 04:59:46.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:46.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:46.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:46.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:46.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:46.954][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:59:46.956][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:59:46.957][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:59:46.959][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:59:46.960][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:59:46.961][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:59:46.963][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:59:46.964][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:59:46.966][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:59:46.967][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:59:46.968][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:59:46.970][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:59:46.971][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:59:46.972][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:59:46.974][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:59:46.975][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:59:46.977][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:59:46.978][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:59:46.979][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:59:46.981][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:59:46.982][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:59:46.983][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:59:46.985][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:59:46.986][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:59:46.988][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:59:46.989][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:59:46.990][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:59:46.992][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:59:46.993][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:59:46.994][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:59:46.996][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:59:46.997][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:59:46.999][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:59:47.000][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:59:47.001][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:59:47.002][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:59:47.004][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:59:47.005][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:59:47.006][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:59:47.008][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:59:47.009][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:59:47.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:59:47.012][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:59:47.013][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:59:47.014][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:59:47.016][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:59:47.017][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:59:47.018][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:59:47.020][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:59:47.021][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:59:47.022][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:59:47.024][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:59:47.025][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:59:47.026][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:59:47.028][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:59:47.029][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:59:47.037][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:59:47.038][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:59:47.040][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:59:47.041][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:59:47.042][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:59:47.044][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:59:47.045][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:59:47.046][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:59:47.047][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:59:47.049][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:59:47.050][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:59:47.051][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:59:47.053][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:59:47.054][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:59:47.055][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:59:47.056][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:59:47.058][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:59:47.059][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:59:47.060][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:59:47.062][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:59:47.063][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:59:47.064][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:59:47.065][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:59:47.067][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:59:47.068][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:59:47.069][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:59:47.071][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:59:47.072][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:59:47.073][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:59:47.074][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:59:47.075][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.077][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.102][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[2023-04-12 04:59:47.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.143][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[2023-04-12 04:59:47.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:59:47.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.181][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-12 04:59:47.183][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-12 04:59:47.185][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:47.186][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:59:47.187][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:47.188][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:59:47.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:47.190][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:59:47.191][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:47.192][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-12 04:59:47.193][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:59:47.194][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:59:47.195][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:47.196][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-12 04:59:47.196][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-12 04:59:47.197][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-12 04:59:47.199][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:59:47.199][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:59:47.199][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:59:47.199][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:59:47.200][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:59:47.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:47.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:47.203][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:59:47.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:59:47.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:59:47.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:59:47.207][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:47.207][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-12 04:59:47.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:59:47.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:59:47.210][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:59:47.211][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-12 04:59:47.211][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-12 04:59:47.212][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:59:47.214][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:59:47.216][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-12 04:59:47.217][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:59:47.219][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:59:47.220][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:59:47.224][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-12 04:59:47.225][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-12 04:59:47.226][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-12 04:59:47.228][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-12 04:59:47.229][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:59:47.230][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:59:47.231][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-12 04:59:47.232][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-12 04:59:47.233][biodb::testThat]
biodb.INFO [2023-04-12 04:59:47.234][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-04-12 04:59:47.235][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:47.236][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:47.240][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-12 04:59:47.243][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:47.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-12 04:59:47.246][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:47.247][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-12 04:59:47.251][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-12 04:59:47.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:47.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-04-12 04:59:47.257][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:47.258][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-04-12 04:59:47.261][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-04-12 04:59:47.262][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:47.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-04-12 04:59:47.265][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:47.266][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:47.267][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:47.268][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-12 04:59:47.269][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:47.270][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:47.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:47.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:47.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:47.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:47.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:47.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:47.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:47.283][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-04-12 04:59:47.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:47.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:47.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-04-12 04:59:51.428][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-04-12 04:59:52.310][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:52.318][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-04-12 04:59:52.329][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-04-12 04:59:52.340][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-04-12 04:59:52.344][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:52.366][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:59:52.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-12 04:59:52.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:52.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:52.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:52.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:52.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:52.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:52.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:52.383][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.386][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.396][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:52.397][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:52.398][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.399][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.401][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-12 04:59:52.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-12 04:59:52.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.408][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:52.410][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:52.410][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.411][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:52.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:52.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.421][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:59:52.423][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:59:52.424][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.426][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.428][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:59:52.429][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:59:52.430][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.431][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.433][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:52.434][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:52.434][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.435][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.437][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:52.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:52.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.444][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:52.445][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:52.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.447][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.449][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-12 04:59:52.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:52.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.464][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:52.467][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:52.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.471][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:52.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:52.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.485][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:52.486][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:52.487][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.488][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:52.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:52.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.499][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:52.501][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:52.502][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.503][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.504][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-12 04:59:52.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-12 04:59:52.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.513][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:52.515][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:52.516][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.517][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.519][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:59:52.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:59:52.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:52.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:52.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:52.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:52.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:52.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:52.576][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-04-12 04:59:52.578][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:59:52.580][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-12 04:59:52.581][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-12 04:59:52.582][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:59:52.583][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:52.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:52.585][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:52.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:52.587][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:52.588][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
>
> proc.time()
user system elapsed
24.516 0.811 74.460
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.019 | 0.065 | 3.273 | |
| ChebiEntry | 0.207 | 0.000 | 0.206 | |