Pierrick Roger
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_14 |
| git_last_commit: 35326c0 |
| git_last_commit_date: 2021-10-27 06:00:18 -0400 (Wed, 27 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:07 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the biodbChebi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 176/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.0.1 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodbChebi |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biodbChebi_1.0.1.tar.gz |
| StartedAt: 2022-04-12 06:34:30 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 06:36:25 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 115.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biodbChebi_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/biodbChebi.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbChebi/DESCRIPTION’ ... OK * this is package ‘biodbChebi’ version ‘1.0.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbChebi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 [2022-04-12 06:35:11.966][biodb::testContext]
biodb.INFO [2022-04-12 06:35:11.968][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:35:11.969][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-04-12 06:35:11.970][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:35:11.971][biodb::testContext]
biodb.INFO [2022-04-12 06:35:11.993][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:35:11.995][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 06:35:12.003][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:35:12.004][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 06:35:12.005][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 06:35:12.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.009][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 06:35:12.029][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 06:35:12.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.032][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[2022-04-12 06:35:12.035][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 06:35:12.036][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 06:35:12.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.039][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 06:35:12.040][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 06:35:12.041][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 06:35:12.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.045][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 06:35:12.046][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 06:35:12.047][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 06:35:12.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.051][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 06:35:12.052][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 06:35:12.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.055][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 06:35:12.061][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 06:35:12.063][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 06:35:12.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.067][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 06:35:12.068][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 06:35:12.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.071][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 06:35:12.072][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 06:35:12.073][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 06:35:12.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.077][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:35:12.078][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 06:35:12.079][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 06:35:12.080][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 06:35:12.081][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 06:35:12.082][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 06:35:12.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.086][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 06:35:12.087][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 06:35:12.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.091][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 06:35:12.092][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 06:35:12.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.095][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 06:35:12.096][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 06:35:12.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.100][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 06:35:12.101][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 06:35:12.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.104][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 06:35:12.106][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 06:35:12.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.109][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:35:12.110][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 06:35:12.116][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-04-12 06:35:12.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.120][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 06:35:12.121][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 06:35:12.122][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 06:35:12.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.129][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 06:35:12.167][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.185][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 06:35:12.186][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.188][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:35:12.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.190][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.191][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.192][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.193][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:35:12.194][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:35:12.195][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.196][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 06:35:12.197][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:35:12.198][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.199][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.200][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:35:12.200][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:35:12.200][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:35:12.200][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:35:12.200][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:35:12.201][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:35:12.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:35:12.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.207][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.208][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.209][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:35:12.210][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:35:12.211][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.212][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.213][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 06:35:12.215][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.216][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:35:12.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.218][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:35:12.219][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.220][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.221][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.239][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.240][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:35:12.241][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:35:12.242][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.243][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 06:35:12.244][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:35:12.245][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.246][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.246][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:35:12.246][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:35:12.246][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:35:12.246][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:35:12.246][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:35:12.247][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:35:12.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.250][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:35:12.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.253][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.254][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.255][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:35:12.256][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:35:12.257][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.258][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.259][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 06:35:12.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.262][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 06:35:12.263][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.264][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:35:12.265][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.266][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.267][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.268][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.269][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:35:12.270][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:35:12.271][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.272][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 06:35:12.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:35:12.274][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.275][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.276][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.277][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:35:12.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.280][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:35:12.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.285][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:35:12.287][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:35:12.288][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.289][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.290][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 06:35:12.292][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.293][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:35:12.294][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:35:12.296][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.298][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.299][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.300][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:35:12.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:35:12.302][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.304][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 06:35:12.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:35:12.306][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.307][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.308][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.309][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:35:12.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:35:12.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.316][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:35:12.318][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:35:12.319][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.320][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:35:12.325][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:35:12.326][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.327][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[2022-04-12 06:35:12.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.401][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 06:35:12.406][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 06:35:12.408][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 06:35:12.409][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 06:35:12.410][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:35:12.412][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 06:35:12.413][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 06:35:12.414][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 06:35:12.416][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 06:35:12.417][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 06:35:12.418][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:35:12.419][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 06:35:12.421][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 06:35:12.422][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 06:35:12.423][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 06:35:12.424][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 06:35:12.426][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 06:35:12.427][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 06:35:12.428][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:35:12.430][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 06:35:12.431][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 06:35:12.432][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 06:35:12.433][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 06:35:12.435][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 06:35:12.436][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 06:35:12.437][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 06:35:12.439][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 06:35:12.440][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 06:35:12.441][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 06:35:12.442][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 06:35:12.444][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 06:35:12.445][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 06:35:12.446][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 06:35:12.447][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 06:35:12.449][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 06:35:12.450][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 06:35:12.451][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 06:35:12.452][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 06:35:12.454][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 06:35:12.455][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 06:35:12.456][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 06:35:12.457][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 06:35:12.459][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 06:35:12.460][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 06:35:12.461][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 06:35:12.463][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 06:35:12.464][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 06:35:12.465][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 06:35:12.466][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 06:35:12.468][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 06:35:12.469][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 06:35:12.470][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 06:35:12.472][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 06:35:12.473][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 06:35:12.474][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 06:35:12.476][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 06:35:12.477][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 06:35:12.479][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 06:35:12.480][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 06:35:12.481][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 06:35:12.483][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 06:35:12.484][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 06:35:12.492][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 06:35:12.494][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 06:35:12.495][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 06:35:12.496][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 06:35:12.497][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:35:12.499][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:35:12.500][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 06:35:12.501][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 06:35:12.502][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 06:35:12.504][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 06:35:12.505][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 06:35:12.506][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 06:35:12.507][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 06:35:12.509][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 06:35:12.510][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 06:35:12.511][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 06:35:12.512][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 06:35:12.514][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 06:35:12.515][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 06:35:12.516][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 06:35:12.517][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 06:35:12.523][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 06:35:12.524][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:35:12.528][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:35:12.528][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.530][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.563][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[2022-04-12 06:35:12.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:35:12.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:12.632][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 06:35:12.641][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 06:35:12.644][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.645][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.647][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:35:12.648][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.649][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.650][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 06:35:12.651][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 06:35:12.652][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:35:12.653][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.654][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 06:35:12.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 06:35:12.656][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 06:35:12.657][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 06:35:12.658][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:35:12.658][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:35:12.658][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:35:12.659][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 06:35:12.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:35:12.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:35:12.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:35:12.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:35:12.665][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:12.665][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 06:35:12.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:35:12.667][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:35:12.667][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 06:35:12.668][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 06:35:12.668][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 06:35:12.674][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:35:12.676][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:35:12.677][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 06:35:12.679][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:35:12.680][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:35:12.682][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:35:12.707][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 06:35:12.709][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 06:35:12.713][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 06:35:12.718][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 06:35:12.722][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:35:12.723][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:35:12.725][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 06:35:12.726][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 06:35:12.772][biodb::testThat]
biodb.INFO [2022-04-12 06:35:12.773][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2022-04-12 06:35:12.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:12.775][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:12.780][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.14-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2022-04-12 06:35:12.793][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:12.798][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:12.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:12.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:12.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:12.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:12.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:12.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:12.813][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.TRACE[2022-04-12 06:35:12.824][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:12.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:12.826][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.827][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:12.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.854][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:12.855][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:12.856][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.857][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.881][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:12.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:12.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.896][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:12.897][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:12.898][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.899][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:12.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:12.917][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:12.918][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.919][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:12.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:12.937][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:12.938][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.938][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:12.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:12.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:12.957][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:12.958][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.959][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:12.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:12.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.975][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:12.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:12.978][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.978][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.980][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:12.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:12.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:12.995][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:12.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.006][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.007][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.022][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.023][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.024][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.025][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.039][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:13.040][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.041][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.042][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.043][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:13.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.056][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.058][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.058][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.059][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:13.152][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2022-04-12 06:35:13.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.216][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 06:35:13.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 06:35:13.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.220][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 06:35:13.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 06:35:13.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.223][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 06:35:13.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 06:35:13.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.227][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 06:35:13.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 06:35:13.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.338][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.339][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.340][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.341][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.365][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.367][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.368][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:13.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.393][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.396][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.396][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.418][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.422][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.424][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.425][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.479][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.480][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.481][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.482][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.506][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.508][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.509][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.521][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.525][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.529][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.533][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.535][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.536][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.537][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.548][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.556][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.560][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.561][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.562][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.563][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.564][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.575][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.579][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.583][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.589][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.590][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.603][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.616][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.618][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.618][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.643][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.644][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.645][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.646][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.670][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.671][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.672][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.673][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.687][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.690][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.691][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.704][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.705][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.706][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.707][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.713][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.714][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.715][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.716][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.722][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.723][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.724][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.725][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.731][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.732][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.733][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.734][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.740][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.741][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:13.742][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.743][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.748][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.749][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:13.750][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.751][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.756][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.757][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:13.758][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.759][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.764][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.765][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:13.766][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.766][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.771][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:13.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:13.773][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.774][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.779][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:13.780][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:13.781][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.782][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:13.788][biodb::testThat]
biodb.INFO [2022-04-12 06:35:13.789][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-04-12 06:35:13.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:13.791][biodb::testThat]
biodb.DEBUG[2022-04-12 06:35:13.804][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2022-04-12 06:35:13.812][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:13.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2022-04-12 06:35:13.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:13.819][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2022-04-12 06:35:13.820][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:13.875][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:13.877][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:13.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:13.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:13.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:13.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:13.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:13.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:13.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:13.887][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.889][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.890][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:13.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.930][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.931][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.932][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.933][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.935][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:13.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:13.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.949][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.950][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.951][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.952][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:13.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:13.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.967][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.970][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.970][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.985][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.986][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.987][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.988][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:13.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:13.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:13.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.004][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:14.005][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:14.006][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.007][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.008][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:14.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:14.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.022][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:14.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:14.024][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.025][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:14.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:14.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.040][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:14.041][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:14.042][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.043][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:14.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.057][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:14.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:14.059][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.060][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.061][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:14.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:14.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.074][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:14.075][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:14.076][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.077][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.078][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:14.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:14.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.092][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:14.093][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:14.094][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.095][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.097][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:14.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:14.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:14.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:14.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:14.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:14.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:14.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:14.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:14.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:14.166][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2022-04-12 06:35:14.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-04-12 06:35:14.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-04-12 06:35:14.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-04-12 06:35:14.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-04-12 06:35:14.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-04-12 06:35:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-04-12 06:35:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:14.184][biodb::testThat]
biodb.INFO [2022-04-12 06:35:14.185][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2022-04-12 06:35:14.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:14.187][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:14.191][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:14.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:14.193][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.194][ef$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:14.195][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2022-04-12 06:35:14.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:14.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:14.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:14.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:14.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:14.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:14.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:14.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:14.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:14.234][function(conn, opt)] With value "squalene".
biodb.DEBUG[2022-04-12 06:35:14.248][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 06:35:14.264][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:14.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 06:35:14.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:14.282][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 06:35:14.303][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[2022-04-12 06:35:14.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:14.307][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:14.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:15.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:16.277][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:16.307][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2022-04-12 06:35:16.373][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2022-04-12 06:35:16.385][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2022-04-12 06:35:16.398][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:16.399][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:16.400][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.401][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.402][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.403][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.404][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.405][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:16.407][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.408][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2022-04-12 06:35:16.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:16.410][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:16.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:16.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:16.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:16.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:16.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:16.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:16.503][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:16.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:16.506][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:16.508][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2022-04-12 06:35:16.524][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.525][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2022-04-12 06:35:16.526][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:16.527][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:16.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:16.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:16.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:16.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:16.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 06:35:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 06:35:16.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 06:35:16.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 06:35:16.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:16.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:16.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:16.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:16.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:16.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:16.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.664][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 06:35:16.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 06:35:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 06:35:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 06:35:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 06:35:16.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:16.678][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.679][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-04-12 06:35:16.679][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:16.680][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.685][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.686][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-04-12 06:35:16.687][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:16.688][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.693][biodb::testThat]
biodb.INFO [2022-04-12 06:35:16.694][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2022-04-12 06:35:16.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:16.695][biodb::testThat]
biodb.DEBUG[2022-04-12 06:35:16.698][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2022-04-12 06:35:17.366][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2022-04-12 06:35:18.694][biodb::testThat]
biodb.INFO [2022-04-12 06:35:18.696][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2022-04-12 06:35:18.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:18.700][biodb::testThat]
biodb.DEBUG[2022-04-12 06:35:19.185][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.INFO [2022-04-12 06:35:19.649][biodb::testThat]
biodb.INFO [2022-04-12 06:35:19.651][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2022-04-12 06:35:19.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:19.654][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:19.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:19.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:19.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:19.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:19.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:19.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:19.762][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:19.767][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:19.769][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:19.771][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:19.773][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 06:35:19.796][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:19.801][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:19.804][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:19.805][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:19.806][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2022-04-12 06:35:19.821][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 06:35:19.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 06:35:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:19.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:19.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:19.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:19.884][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:19.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:19.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:19.924][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:20.358][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:20.810][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:20.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content"
biodb.TRACE[2022-04-12 06:35:20.840][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.request"
biodb.DEBUG[2022-04-12 06:35:20.848][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[2022-04-12 06:35:20.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:20.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:20.854][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:21.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:21.752][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:21.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content"
biodb.TRACE[2022-04-12 06:35:21.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.request"
biodb.DEBUG[2022-04-12 06:35:21.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:21.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:21.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:21.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:21.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:21.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:21.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:21.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:21.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:21.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:21.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:21.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:21.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:21.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:21.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:21.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:21.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:21.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:21.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:21.862][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:21.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:21.866][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:21.868][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:22.300][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:22.743][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:22.753][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content"
biodb.TRACE[2022-04-12 06:35:22.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.request"
biodb.DEBUG[2022-04-12 06:35:22.806][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[2022-04-12 06:35:22.809][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:22.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:22.812][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:22.813][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 06:35:22.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:22.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:22.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:22.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:22.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:22.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:22.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:22.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:22.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:22.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:22.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:22.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:22.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:22.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:22.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:22.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:22.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:22.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:22.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:22.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:22.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:22.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:22.863][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2022-04-12 06:35:22.906][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:22.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2022-04-12 06:35:22.909][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:22.910][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:22.911][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:22.912][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:22.913][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:22.914][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:22.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:22.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:22.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:22.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:22.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:22.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:22.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:22.923][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2022-04-12 06:35:22.926][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:22.927][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:22.928][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2022-04-12 06:35:23.369][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2022-04-12 06:35:23.826][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:23.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2022-04-12 06:35:23.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2022-04-12 06:35:23.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2022-04-12 06:35:23.869][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:23.886][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:23.888][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:23.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:23.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:23.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:23.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:23.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:23.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:23.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:23.898][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:23.899][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:23.900][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.901][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:23.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:23.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.909][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:23.910][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:23.911][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.912][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.913][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:23.914][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:23.915][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.916][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.917][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:23.918][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:23.919][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.920][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.921][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:23.922][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:23.923][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.924][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.925][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:23.926][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:23.927][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.928][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.929][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:23.930][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:23.931][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.931][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:23.934][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:23.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.935][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.936][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:23.937][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:23.938][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.939][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:23.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:23.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.948][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:23.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:23.950][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.951][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.952][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:23.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.960][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:23.961][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:23.962][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.963][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:23.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:23.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:23.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:23.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:23.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:23.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:23.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:23.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:23.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:23.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:23.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:23.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:23.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:23.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:24.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:24.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:24.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:24.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:24.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:24.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:24.013][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2022-04-12 06:35:24.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:24.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:24.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:24.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:24.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:24.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:24.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:24.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:24.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:24.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:24.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:24.047][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2022-04-12 06:35:24.048][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:24.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2022-04-12 06:35:24.051][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:24.052][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:24.053][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:24.054][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:24.054][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:24.055][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:24.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:24.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:24.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:24.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:24.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:24.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:24.073][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[2022-04-12 06:35:24.074][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2022-04-12 06:35:24.077][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:24.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:24.079][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2022-04-12 06:35:24.623][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2022-04-12 06:35:25.333][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:25.347][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2022-04-12 06:35:25.381][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2022-04-12 06:35:25.400][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2022-04-12 06:35:25.408][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:25.440][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:25.442][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:25.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:25.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:25.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:25.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:25.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:25.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:25.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:25.458][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.460][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.461][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.462][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.478][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:25.481][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:25.483][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.485][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.486][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:25.487][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:25.488][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.489][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.490][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:25.491][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:25.492][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.493][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.494][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:25.495][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:25.496][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.497][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.499][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:25.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:25.501][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.501][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.503][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:25.504][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.505][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.505][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.507][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:25.508][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:25.509][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.509][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.511][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:25.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:25.512][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.513][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:25.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:25.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.522][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:25.523][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:25.524][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.525][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.526][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:25.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:25.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.533][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:25.534][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:25.535][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.536][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:25.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:25.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:25.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:25.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:25.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:25.578][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2022-04-12 06:35:25.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:25.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:25.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:25.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:25.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:25.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:25.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:25.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:25.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:25.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:25.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:25.608][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2022-04-12 06:35:25.609][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:25.611][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2022-04-12 06:35:25.612][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:25.613][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:25.614][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:25.615][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:25.616][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:25.617][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:25.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:25.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:25.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:25.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:25.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:25.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:25.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:25.626][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2022-04-12 06:35:25.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:25.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:25.631][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2022-04-12 06:35:26.068][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2022-04-12 06:35:26.610][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:26.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2022-04-12 06:35:26.634][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2022-04-12 06:35:26.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2022-04-12 06:35:26.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:26.685][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:26.687][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:26.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:26.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:26.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:26.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:26.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:26.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:26.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:26.719][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.721][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.722][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.723][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.732][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:26.733][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:26.734][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.735][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.737][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:26.738][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:26.739][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.740][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.741][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:26.742][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:26.743][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.744][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.745][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:26.746][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:26.747][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.748][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:26.751][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:26.752][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.753][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.754][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:26.755][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.756][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.757][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.758][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:26.759][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:26.760][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.761][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.762][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:26.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:26.765][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.765][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:26.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:26.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:26.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:26.777][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.778][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.779][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:26.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.787][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:26.789][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:26.790][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.790][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:26.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:26.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:26.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:26.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:26.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:26.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:26.835][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2022-04-12 06:35:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:26.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:26.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:26.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:26.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:26.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:26.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:26.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:26.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:26.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:26.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:26.865][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2022-04-12 06:35:26.866][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:26.868][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2022-04-12 06:35:26.869][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:26.870][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:26.871][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:26.872][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:26.873][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:26.874][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:26.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:26.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:26.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:26.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:26.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:26.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:26.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:26.885][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2022-04-12 06:35:26.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:26.889][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:26.890][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2022-04-12 06:35:27.361][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2022-04-12 06:35:27.924][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:27.937][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2022-04-12 06:35:27.957][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2022-04-12 06:35:27.975][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2022-04-12 06:35:27.984][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:28.006][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:28.007][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:28.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:28.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:28.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:28.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:28.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:28.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:28.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:28.017][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.018][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.019][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.020][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.028][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:28.029][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:28.030][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.031][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.032][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:28.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:28.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.039][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:28.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:28.041][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.042][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:28.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.051][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:28.052][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:28.052][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.053][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:28.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:28.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:28.063][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:28.064][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.065][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:28.082][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:28.083][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.083][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.085][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:28.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:28.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.092][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:28.093][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.094][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.095][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:28.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.104][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:28.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:28.105][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.106][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:28.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:28.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.115][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:28.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:28.117][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.118][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:28.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:28.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.128][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:28.129][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:28.130][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.131][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:28.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:28.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:28.141][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:28.142][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.142][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:28.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:28.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:28.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:28.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:28.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:28.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:28.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:28.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:28.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:28.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:28.193][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2022-04-12 06:35:28.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:28.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:28.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:28.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:28.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:28.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:28.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:28.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:28.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:28.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:28.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:28.211][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2022-04-12 06:35:28.212][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:28.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2022-04-12 06:35:28.215][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:28.216][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:28.217][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:28.218][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:28.218][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:28.219][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:28.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:28.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:28.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:28.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:28.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:28.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:28.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:28.228][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2022-04-12 06:35:28.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:28.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:28.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2022-04-12 06:35:28.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2022-04-12 06:35:29.142][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:29.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2022-04-12 06:35:29.162][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2022-04-12 06:35:29.174][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2022-04-12 06:35:29.178][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:29.194][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:29.195][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:29.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:29.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:29.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:29.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:29.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:29.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:29.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:29.204][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.205][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.206][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.207][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.215][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:29.216][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:29.217][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.218][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.219][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:29.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:29.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.226][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:29.227][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:29.228][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.229][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.238][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:29.240][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:29.240][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.241][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:29.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:29.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.250][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:29.251][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:29.252][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.252][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:29.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.261][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:29.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:29.270][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.271][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:29.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:29.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.279][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:29.280][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.281][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.282][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.290][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:29.291][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:29.292][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.293][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:29.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:29.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.301][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:29.302][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:29.303][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.304][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:29.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:29.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.313][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:29.314][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:29.315][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.315][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:29.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.324][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:29.325][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:29.325][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.326][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.327][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:29.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:29.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:29.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:29.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:29.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:29.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:29.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:29.375][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2022-04-12 06:35:29.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:29.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:29.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:29.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:29.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:29.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:29.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:29.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:29.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:29.393][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2022-04-12 06:35:29.394][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:29.395][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2022-04-12 06:35:29.397][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:29.398][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:29.398][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:29.399][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:29.400][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:29.401][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:29.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:29.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:29.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:29.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:29.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:29.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:29.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:29.410][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2022-04-12 06:35:29.412][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:29.413][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:29.414][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2022-04-12 06:35:29.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2022-04-12 06:35:30.308][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:30.317][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2022-04-12 06:35:30.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2022-04-12 06:35:30.342][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2022-04-12 06:35:30.347][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:30.364][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:30.365][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:30.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:30.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:30.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:30.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:30.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:30.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:30.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:30.375][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.377][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.378][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.386][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:30.387][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:30.388][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.389][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.391][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:30.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:30.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.398][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:30.399][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:30.400][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.401][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:30.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:30.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.410][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:30.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:30.412][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.413][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:30.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:30.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.421][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:30.422][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:30.423][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.424][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:30.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:30.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.433][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:30.434][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:30.435][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.436][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.437][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:30.438][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.439][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.440][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.441][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:30.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.458][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:30.459][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:30.460][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.460][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:30.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:30.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.469][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:30.470][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:30.471][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.472][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:30.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:30.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.480][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:30.481][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:30.482][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.483][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:30.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:30.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.492][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:30.493][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:30.494][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.495][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:30.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:30.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:30.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:30.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:30.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:30.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:30.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:30.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:30.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:30.546][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2022-04-12 06:35:30.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:30.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:30.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:30.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:30.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:30.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:30.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:30.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:30.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:30.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:30.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:30.566][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2022-04-12 06:35:30.567][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:30.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2022-04-12 06:35:30.570][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:30.571][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:30.572][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:30.573][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:30.574][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:30.575][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:30.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:30.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:30.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:30.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:30.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:30.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:30.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:30.585][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2022-04-12 06:35:30.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:30.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:30.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2022-04-12 06:35:31.040][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2022-04-12 06:35:31.476][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:31.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2022-04-12 06:35:31.497][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2022-04-12 06:35:31.509][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2022-04-12 06:35:31.514][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:31.531][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:31.532][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:31.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:31.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:31.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:31.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:31.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:31.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:31.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:31.541][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.542][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.543][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.544][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.552][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:31.553][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:31.554][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.554][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.556][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:31.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:31.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.563][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:31.564][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:31.564][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.565][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:31.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:31.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:31.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:31.575][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.576][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:31.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:31.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:31.585][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:31.585][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.586][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:31.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:31.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.594][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:31.595][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:31.596][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.597][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.598][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:31.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.600][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.600][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:31.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.608][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:31.609][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:31.610][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.611][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:31.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:31.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.619][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:31.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:31.625][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.627][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:31.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:31.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.635][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:31.636][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:31.637][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.638][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.639][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:31.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:31.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.646][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:31.646][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:31.647][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.648][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.649][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:31.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:31.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:31.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:31.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:31.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:31.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:31.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:31.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:31.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:31.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:31.693][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2022-04-12 06:35:31.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:31.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:31.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:31.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:31.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:31.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:31.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:31.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:31.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:31.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:31.711][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2022-04-12 06:35:31.712][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:31.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2022-04-12 06:35:31.714][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:31.715][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:31.716][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:31.717][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:31.718][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:31.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:31.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:31.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:31.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:31.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:31.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:31.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:31.727][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[2022-04-12 06:35:31.728][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2022-04-12 06:35:31.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:31.731][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:31.733][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2022-04-12 06:35:32.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2022-04-12 06:35:32.597][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:32.606][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2022-04-12 06:35:32.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2022-04-12 06:35:32.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2022-04-12 06:35:32.634][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:32.650][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:32.651][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:32.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:32.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:32.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:32.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:32.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:32.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:32.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:32.660][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.661][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.662][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.663][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.671][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:32.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:32.673][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.674][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.675][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:32.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:32.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.683][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:32.684][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:32.684][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.685][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:32.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:32.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.694][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:32.695][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:32.696][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.697][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:32.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:32.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.705][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:32.706][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:32.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.708][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:32.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:32.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:32.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:32.719][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.720][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.721][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:32.722][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.723][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.724][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.725][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:32.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.732][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:32.733][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:32.734][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.735][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:32.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:32.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.744][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:32.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:32.746][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.746][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:32.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:32.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.755][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:32.756][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:32.757][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.757][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.759][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:32.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:32.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.771][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:32.772][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:32.772][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.773][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.774][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:32.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:32.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:32.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:32.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:32.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:32.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:32.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:32.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:32.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:32.822][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2022-04-12 06:35:32.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:32.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:32.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:32.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:32.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:32.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:32.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:32.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:32.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:32.841][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2022-04-12 06:35:32.841][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:32.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2022-04-12 06:35:32.844][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:32.845][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:32.846][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:32.847][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:32.848][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:32.849][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:32.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:32.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:32.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:32.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:32.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:32.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:32.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:32.858][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2022-04-12 06:35:32.860][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:32.861][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:32.863][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2022-04-12 06:35:33.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2022-04-12 06:35:33.724][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:33.733][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2022-04-12 06:35:33.756][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2022-04-12 06:35:33.769][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2022-04-12 06:35:33.774][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:33.793][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:33.794][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:33.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:33.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:33.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:33.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:33.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:33.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:33.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:33.804][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.805][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.805][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.806][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.822][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:33.823][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:33.824][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.825][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.827][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:33.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:33.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.835][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:33.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:33.837][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.838][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:33.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:33.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.847][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:33.848][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:33.849][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.850][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:33.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:33.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.860][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:33.861][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:33.862][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.862][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:33.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.872][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:33.873][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:33.874][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.875][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.876][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:33.878][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:33.879][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.880][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.881][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:33.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:33.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.889][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:33.891][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:33.892][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.893][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:33.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:33.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.902][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:33.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:33.905][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.905][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:33.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.915][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:33.916][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:33.917][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.918][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.919][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:33.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:33.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.927][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:33.928][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:33.929][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.930][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:33.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:33.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:33.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:33.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:33.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:33.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:33.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:33.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:33.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:33.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:33.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:33.995][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2022-04-12 06:35:33.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:33.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:33.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:33.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:34.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:34.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:34.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:34.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:34.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:34.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:34.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:34.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:34.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:34.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:34.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:34.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:34.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:34.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:34.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:34.015][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2022-04-12 06:35:34.016][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:34.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2022-04-12 06:35:34.018][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:34.019][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:34.020][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:34.021][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:34.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:34.023][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:34.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:34.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:34.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:34.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:34.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:34.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:34.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:34.032][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2022-04-12 06:35:34.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:34.036][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:34.037][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2022-04-12 06:35:34.459][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2022-04-12 06:35:34.917][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:34.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2022-04-12 06:35:34.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2022-04-12 06:35:34.960][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2022-04-12 06:35:34.965][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:34.982][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:34.984][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:34.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:34.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:34.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:34.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:34.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:34.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:34.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:34.993][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:34.995][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:34.995][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:34.996][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:34.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:34.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:34.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.006][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:35.007][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:35.008][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.009][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:35.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.018][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:35.019][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:35.019][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.020][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:35.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:35.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.029][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:35.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:35.031][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.032][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:35.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:35.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.040][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:35.041][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:35.042][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.043][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:35.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:35.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.052][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:35.053][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:35.054][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.055][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.056][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:35.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.058][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.059][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.060][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:35.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.069][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:35.070][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:35.071][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.072][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:35.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.082][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:35.083][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:35.084][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.084][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:35.095][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:35.096][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.097][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.098][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:35.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:35.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.107][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:35.108][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:35.108][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.109][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:35.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:35.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:35.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:35.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:35.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:35.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:35.166][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2022-04-12 06:35:35.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:35.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:35.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:35.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:35.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:35.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:35.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:35.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:35.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:35.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:35.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:35.185][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2022-04-12 06:35:35.186][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:35.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2022-04-12 06:35:35.188][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:35.189][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:35.190][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:35.191][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:35.192][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:35.193][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:35.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:35.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:35.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:35.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:35.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:35.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:35.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:35.203][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2022-04-12 06:35:35.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:35.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:35.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2022-04-12 06:35:35.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2022-04-12 06:35:36.187][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:36.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2022-04-12 06:35:36.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2022-04-12 06:35:36.220][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2022-04-12 06:35:36.224][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:36.247][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:36.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:36.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:36.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:36.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:36.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:36.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:36.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:36.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:36.257][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.259][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.260][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.268][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:36.269][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:36.270][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.271][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.272][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:36.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:36.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.280][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:36.281][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:36.281][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.282][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:36.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:36.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.291][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:36.292][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:36.293][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.294][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:36.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:36.297][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.297][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.299][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:36.300][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:36.300][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.301][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.302][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:36.303][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.304][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.305][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.306][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:36.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.314][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:36.315][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:36.316][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.317][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:36.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:36.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.325][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:36.326][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:36.327][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.328][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:36.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:36.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.337][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:36.338][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:36.339][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.340][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.341][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:36.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:36.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.349][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:36.350][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:36.351][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.352][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:36.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:36.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:36.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:36.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:36.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:36.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:36.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:36.394][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2022-04-12 06:35:36.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:36.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:36.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:36.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:36.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:36.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:36.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:36.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:36.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:36.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:36.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:36.418][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2022-04-12 06:35:36.419][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:36.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2022-04-12 06:35:36.422][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:36.423][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:36.424][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:36.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:36.426][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:36.427][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:36.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:36.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:36.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:36.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:36.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:36.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:36.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:36.436][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2022-04-12 06:35:36.439][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:36.440][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:36.441][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2022-04-12 06:35:36.882][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2022-04-12 06:35:37.489][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:37.497][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2022-04-12 06:35:37.510][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2022-04-12 06:35:37.523][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2022-04-12 06:35:37.528][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:37.544][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:37.546][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:37.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:37.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:37.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:37.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:37.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:37.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:37.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:37.555][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.556][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.557][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.566][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:37.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:37.568][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.568][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:37.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:37.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.584][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:37.585][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:37.586][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.587][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:37.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:37.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.595][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:37.596][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:37.597][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.597][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.598][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:37.599][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:37.600][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.601][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.602][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:37.603][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:37.604][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.605][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.606][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:37.607][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.608][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.609][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.610][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:37.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.618][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:37.619][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:37.620][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.621][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:37.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:37.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.629][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:37.630][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:37.631][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.632][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:37.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:37.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.640][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:37.641][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:37.642][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.643][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:37.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:37.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.651][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:37.652][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:37.653][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.654][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:37.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:37.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:37.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:37.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:37.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:37.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:37.697][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2022-04-12 06:35:37.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:37.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:37.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:37.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:37.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:37.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:37.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:37.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:37.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:37.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:37.716][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2022-04-12 06:35:37.717][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:37.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2022-04-12 06:35:37.720][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:37.721][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:37.722][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:37.723][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:37.724][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:37.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:37.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:37.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:37.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:37.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:37.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:37.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:37.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:37.734][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2022-04-12 06:35:37.737][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:37.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:37.739][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2022-04-12 06:35:38.194][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2022-04-12 06:35:38.628][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:38.637][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2022-04-12 06:35:38.649][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2022-04-12 06:35:38.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2022-04-12 06:35:38.666][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:38.683][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:38.684][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:38.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:38.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:38.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:38.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:38.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:38.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:38.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:38.694][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.696][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.697][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.706][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:38.707][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:38.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.708][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.710][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:38.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:38.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.717][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:38.718][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:38.719][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.720][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:38.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:38.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.729][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:38.730][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:38.731][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.731][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:38.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:38.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.740][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:38.741][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:38.742][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.743][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:38.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:38.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.760][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:38.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:38.762][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.763][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.764][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:38.765][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.766][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.767][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.768][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:38.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.775][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:38.776][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:38.777][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.778][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:38.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:38.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.787][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:38.788][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:38.789][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.790][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:38.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:38.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.799][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:38.800][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:38.801][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.802][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.803][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:38.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:38.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.810][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:38.811][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:38.812][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.813][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.814][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:38.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:38.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:38.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:38.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:38.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:38.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:38.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:38.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:38.863][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2022-04-12 06:35:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:38.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:38.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:38.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:38.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:38.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:38.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:38.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:38.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:38.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:38.882][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2022-04-12 06:35:38.883][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:38.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2022-04-12 06:35:38.885][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:38.886][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:38.887][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:38.888][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:38.889][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:38.890][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:38.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:38.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:38.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:38.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:38.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:38.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:38.899][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[2022-04-12 06:35:38.900][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2022-04-12 06:35:38.903][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:38.903][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:38.905][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2022-04-12 06:35:39.343][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2022-04-12 06:35:39.780][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:39.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2022-04-12 06:35:39.801][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2022-04-12 06:35:39.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2022-04-12 06:35:39.817][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:39.834][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:39.835][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:39.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:39.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:39.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:39.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:39.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:39.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:39.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:39.845][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:39.846][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:39.847][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.848][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:39.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.857][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:39.858][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:39.859][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.860][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.861][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:39.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:39.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.869][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:39.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:39.871][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.872][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:39.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:39.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.881][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:39.882][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:39.882][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.883][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:39.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:39.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.892][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:39.893][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:39.894][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.895][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:39.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:39.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.904][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:39.905][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:39.905][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.906][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.908][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:39.909][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:39.910][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.918][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:39.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.927][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:39.928][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:39.929][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.930][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:39.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:39.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.939][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:39.940][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:39.940][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.941][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:39.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:39.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.950][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:39.951][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:39.952][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.953][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.954][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:39.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:39.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.961][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:39.962][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:39.963][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.964][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:39.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:39.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:39.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:39.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:39.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:39.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:39.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:39.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:39.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:39.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:39.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:39.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:39.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:39.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:39.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:39.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:40.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:40.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:40.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:40.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:40.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:40.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:40.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:40.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:40.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:40.016][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2022-04-12 06:35:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:40.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:40.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:40.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:40.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:40.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:40.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:40.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:40.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:40.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:40.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:40.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:40.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:40.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:40.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:40.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:40.036][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2022-04-12 06:35:40.037][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:40.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2022-04-12 06:35:40.040][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:40.041][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:40.042][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:40.043][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:40.044][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:40.045][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:40.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:40.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:40.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:40.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:40.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:40.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:40.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:40.055][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2022-04-12 06:35:40.057][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:40.058][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:40.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2022-04-12 06:35:40.496][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2022-04-12 06:35:40.936][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:40.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2022-04-12 06:35:40.960][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2022-04-12 06:35:40.973][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2022-04-12 06:35:40.978][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:40.995][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:40.996][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:40.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:40.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:41.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:41.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:41.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:41.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:41.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:41.006][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.007][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.008][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.009][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.018][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:41.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:41.020][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.021][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.022][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:41.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:41.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.030][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:41.031][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:41.032][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.033][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:41.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:41.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.042][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:41.043][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:41.044][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.045][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:41.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:41.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.054][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:41.055][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:41.056][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.057][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:41.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.066][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:41.067][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:41.068][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.069][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.070][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:41.071][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.072][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.073][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.074][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:41.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.082][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:41.083][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:41.083][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.102][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:41.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:41.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.115][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:41.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:41.117][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.118][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:41.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:41.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.128][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:41.129][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:41.130][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.131][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:41.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:41.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:41.141][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:41.142][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.143][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.145][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:41.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:41.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:41.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:41.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:41.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:41.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:41.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:41.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:41.197][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2022-04-12 06:35:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:41.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:41.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:41.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:41.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:41.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:41.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:41.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:41.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:41.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:41.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:41.218][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2022-04-12 06:35:41.219][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:41.221][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2022-04-12 06:35:41.222][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:41.223][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:41.224][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:41.225][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:41.227][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:41.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:41.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:41.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:41.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:41.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:41.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:41.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:41.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:41.238][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2022-04-12 06:35:41.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:41.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:41.244][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2022-04-12 06:35:41.680][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2022-04-12 06:35:42.312][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:42.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2022-04-12 06:35:42.337][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2022-04-12 06:35:42.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2022-04-12 06:35:42.355][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:42.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:42.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:42.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:42.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:42.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:42.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:42.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:42.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:42.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:42.385][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.387][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.388][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.398][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:42.399][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:42.400][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.401][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.410][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:42.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:42.412][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.413][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.415][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:42.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:42.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.423][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:42.424][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:42.425][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.426][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:42.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:42.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.435][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:42.436][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:42.437][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.437][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:42.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:42.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.446][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:42.447][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:42.448][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.449][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.450][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:42.451][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.452][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.453][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.454][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:42.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:42.463][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:42.463][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.464][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:42.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:42.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.473][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:42.474][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:42.481][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.482][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:42.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:42.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:42.493][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.493][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.495][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:42.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:42.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.502][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:42.503][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:42.504][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.505][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.507][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:42.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:42.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:42.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:42.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:42.557][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2022-04-12 06:35:42.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:42.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:42.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:42.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:42.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:42.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:42.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:42.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:42.575][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2022-04-12 06:35:42.576][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:42.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2022-04-12 06:35:42.578][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:42.579][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:42.580][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:42.581][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:42.582][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:42.583][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:42.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:42.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:42.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:42.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:42.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:42.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:42.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:42.592][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2022-04-12 06:35:42.595][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:42.596][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:42.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2022-04-12 06:35:43.032][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2022-04-12 06:35:43.488][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:43.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2022-04-12 06:35:43.513][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2022-04-12 06:35:43.526][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2022-04-12 06:35:43.531][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:43.549][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:43.550][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:43.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.560][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.561][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.562][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.563][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.572][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:43.573][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:43.573][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.574][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.576][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:43.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:43.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.583][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:43.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:43.585][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.586][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:43.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:43.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:43.595][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:43.596][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.597][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:43.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:43.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.606][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:43.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:43.608][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.609][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:43.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.617][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:43.619][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:43.619][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.620][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.621][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:43.622][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.623][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.624][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.625][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:43.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.633][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:43.634][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:43.634][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.635][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:43.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:43.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.644][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:43.645][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:43.646][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.646][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.655][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:43.656][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:43.657][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.663][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.665][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:43.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:43.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.673][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:43.674][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:43.675][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.676][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.677][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:43.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:43.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:43.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:43.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:43.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:43.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:43.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:43.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:43.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.724][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2022-04-12 06:35:43.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.759][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[2022-04-12 06:35:43.762][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:43.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:43.764][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:43.766][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 06:35:43.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.953][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.TRACE[2022-04-12 06:35:43.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:43.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:43.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:43.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:43.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:43.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:43.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:43.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:43.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:43.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:43.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:44.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:44.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:44.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:44.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:44.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:44.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:44.124][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[2022-04-12 06:35:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:44.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:44.221][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[2022-04-12 06:35:44.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:44.225][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:44.226][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:44.801][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:45.295][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:45.309][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1eb5a44d25716d90ff717fcfe93533e3.content"
biodb.TRACE[2022-04-12 06:35:45.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1eb5a44d25716d90ff717fcfe93533e3.request"
biodb.DEBUG[2022-04-12 06:35:45.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:45.346][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:45.348][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:45.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:45.818][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:46.272][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:46.284][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ef91a3654a792571304ae6f83c5871b.content"
biodb.TRACE[2022-04-12 06:35:46.301][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ef91a3654a792571304ae6f83c5871b.request"
biodb.DEBUG[2022-04-12 06:35:46.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:46.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:46.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:46.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:46.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:46.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:46.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:46.318][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2022-04-12 06:35:46.319][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:46.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2022-04-12 06:35:46.321][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:46.322][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:46.323][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:46.324][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:46.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:46.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:46.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:46.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:46.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:46.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:46.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:46.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:46.335][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[2022-04-12 06:35:46.336][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2022-04-12 06:35:46.338][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:46.339][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:46.341][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2022-04-12 06:35:46.841][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2022-04-12 06:35:47.463][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:47.496][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2022-04-12 06:35:47.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2022-04-12 06:35:47.539][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2022-04-12 06:35:47.547][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:47.590][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:47.592][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:47.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:47.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:47.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:47.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:47.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:47.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:47.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:47.607][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.609][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.610][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.623][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:47.625][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:47.626][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.627][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.629][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:47.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:47.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.638][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:47.639][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:47.640][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.641][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:47.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:47.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.652][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:47.653][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:47.654][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.655][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:47.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.665][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:47.666][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:47.667][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.668][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:47.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:47.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.679][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:47.680][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:47.681][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.682][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:47.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:47.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.692][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:47.693][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:47.694][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.695][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.697][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:47.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:47.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.705][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.706][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.708][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.717][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:47.718][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:47.719][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.720][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:47.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:47.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.729][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:47.730][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:47.731][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.732][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.733][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:47.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:47.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.755][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:47.756][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:47.757][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.758][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.759][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:47.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:47.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:47.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:47.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:47.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:47.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:47.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:47.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:47.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:47.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:47.810][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2022-04-12 06:35:47.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:47.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:47.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:47.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:47.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:47.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:47.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:47.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:47.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:47.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:47.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:47.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:47.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:47.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:47.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:47.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:47.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:47.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:47.847][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2022-04-12 06:35:47.848][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:35:47.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2022-04-12 06:35:47.851][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:35:47.852][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:35:47.853][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:35:47.854][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:35:47.855][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:35:47.856][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:35:47.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:47.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:47.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:47.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:47.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:47.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:47.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:47.865][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2022-04-12 06:35:47.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:47.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:47.870][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2022-04-12 06:35:48.297][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2022-04-12 06:35:48.746][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:48.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2022-04-12 06:35:48.765][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2022-04-12 06:35:48.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2022-04-12 06:35:48.781][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:35:48.797][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:35:48.798][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:35:48.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:48.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:48.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:48.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:48.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:48.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:48.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:48.807][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.809][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.810][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.818][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:48.819][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:48.820][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.821][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.822][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:35:48.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:35:48.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.829][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:48.830][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:48.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.832][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:35:48.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:35:48.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.840][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:48.841][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:48.842][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.842][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:35:48.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:35:48.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.850][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:48.851][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:48.852][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.853][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:35:48.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:35:48.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.861][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:48.862][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:35:48.863][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.864][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.865][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:48.866][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:48.867][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.867][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.869][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:35:48.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:48.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.876][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.877][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.878][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.878][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.887][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:48.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:48.888][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.889][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:35:48.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:35:48.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.904][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:48.905][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:48.906][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.907][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:35:48.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:35:48.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.915][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:48.916][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:48.917][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.917][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.919][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:35:48.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:35:48.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:48.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:48.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:48.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:48.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:48.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:48.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:35:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:35:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:48.964][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2022-04-12 06:35:48.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:48.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:48.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:48.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:48.999][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[2022-04-12 06:35:49.001][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:49.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:49.004][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:49.005][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 06:35:49.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.049][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.TRACE[2022-04-12 06:35:49.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.102][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.TRACE[2022-04-12 06:35:49.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.281][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.TRACE[2022-04-12 06:35:49.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.297][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[2022-04-12 06:35:49.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.331][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.TRACE[2022-04-12 06:35:49.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.387][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[2022-04-12 06:35:49.389][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:49.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 06:35:49.392][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:49.393][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 06:35:49.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.528][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[2022-04-12 06:35:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.672][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.TRACE[2022-04-12 06:35:49.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.745][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.TRACE[2022-04-12 06:35:49.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.772][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 06:35:49.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 06:35:49.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:49.782][biodb::testThat]
biodb.INFO [2022-04-12 06:35:49.783][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-04-12 06:35:49.784][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:49.785][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:49.788][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 06:35:49.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 06:35:49.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:49.930][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[2022-04-12 06:35:49.933][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:49.934][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1e3885f0c8b7bc081513880959401862".
biodb.TRACE[2022-04-12 06:35:49.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:49.936][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content".
biodb.DEBUG[2022-04-12 06:35:49.939][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[2022-04-12 06:35:49.942][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:49.943][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4b7e19492b2d1086a5dba1710a3b39b".
biodb.TRACE[2022-04-12 06:35:49.944][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:49.945][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content".
biodb.DEBUG[2022-04-12 06:35:49.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.953][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.TRACE[2022-04-12 06:35:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:49.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:49.966][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[2022-04-12 06:35:49.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:35:49.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d57f841033be8ab371045edb0388ed60".
biodb.TRACE[2022-04-12 06:35:49.970][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:35:49.972][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content".
biodb.DEBUG[2022-04-12 06:35:49.974][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 06:35:49.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:49.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:49.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:49.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:49.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:49.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:49.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:49.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.989][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:49.990][private$selectFields]
biodb.TRACE[2022-04-12 06:35:49.991][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:49.992][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:49.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:49.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.995][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:49.996][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:49.997][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.998][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:49.999][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.000][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.001][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:50.002][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:50.002][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.003][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.004][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.005][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.006][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:50.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.032][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 06:35:50.033][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 06:35:50.034][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 06:35:50.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:50.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:50.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:50.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:50.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:50.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:50.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:50.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:50.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:50.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:50.227][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[2022-04-12 06:35:50.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:50.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:50.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:50.779][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:51.369][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:51.401][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.content"
biodb.TRACE[2022-04-12 06:35:51.435][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.request"
biodb.DEBUG[2022-04-12 06:35:51.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:51.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:51.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:51.455][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:51.937][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:52.509][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-04-12 06:35:52.528][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2022-04-12 06:35:52.546][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.content"
biodb.TRACE[2022-04-12 06:35:52.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.request"
biodb.DEBUG[2022-04-12 06:35:52.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:52.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:52.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:52.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:52.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:52.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:52.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:52.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:52.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:52.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:52.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:52.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:52.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:52.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:52.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:52.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:52.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:52.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:52.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:52.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:52.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:52.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:52.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:52.719][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 06:35:52.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:52.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:52.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:52.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:52.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:52.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:52.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:52.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:52.760][private$selectFields]
biodb.TRACE[2022-04-12 06:35:52.761][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:52.762][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:52.763][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:52.764][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.765][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.766][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.767][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.768][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.769][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.770][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.771][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:52.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:52.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.776][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.777][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.778][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:52.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:52.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:52.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:52.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-04-12 06:35:52.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:52.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:52.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:52.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:52.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:52.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:52.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.047][private$selectFields]
biodb.TRACE[2022-04-12 06:35:53.048][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:53.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:53.049][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.051][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.052][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.053][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.054][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.055][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.056][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.057][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.058][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.067][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.070][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.071][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.072][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:53.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.085][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 06:35:53.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:53.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:53.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:53.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:53.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:53.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:53.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:53.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.101][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.102][private$selectFields]
biodb.TRACE[2022-04-12 06:35:53.103][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:53.104][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:53.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.107][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.108][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.109][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.111][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.112][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.113][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.114][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.116][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.117][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.118][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:53.120][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.121][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.122][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.123][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.125][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:53.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:53.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.145][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-04-12 06:35:53.146][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 06:35:53.147][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 06:35:53.156][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 06:35:53.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 06:35:53.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:53.161][biodb::testThat]
biodb.INFO [2022-04-12 06:35:53.162][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-04-12 06:35:53.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:53.164][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:53.167][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 06:35:53.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 06:35:53.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:53.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:53.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:53.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:53.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:53.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:53.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:53.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:53.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:53.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:53.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:53.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:53.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:53.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:53.318][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:54.036][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:54.581][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:54.600][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content"
biodb.TRACE[2022-04-12 06:35:54.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.request"
biodb.DEBUG[2022-04-12 06:35:54.641][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[2022-04-12 06:35:54.644][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:54.645][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:54.647][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:55.145][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:55.702][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:55.731][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content"
biodb.TRACE[2022-04-12 06:35:55.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.request"
biodb.DEBUG[2022-04-12 06:35:55.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:55.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:55.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:55.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:55.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:55.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:55.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:55.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:55.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:55.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:55.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:55.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:55.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:55.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:55.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:55.812][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:55.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:55.816][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:55.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:56.271][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:56.767][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-04-12 06:35:56.777][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2022-04-12 06:35:56.786][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content"
biodb.TRACE[2022-04-12 06:35:56.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.request"
biodb.DEBUG[2022-04-12 06:35:56.824][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 06:35:56.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:56.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:56.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:56.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:56.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:56.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:56.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:56.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:56.841][private$selectFields]
biodb.TRACE[2022-04-12 06:35:56.842][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:56.843][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:56.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:56.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.846][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.847][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.848][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.849][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.850][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.851][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:56.852][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:56.853][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.855][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.856][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.857][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:56.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:56.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.870][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 06:35:56.871][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 06:35:56.871][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 06:35:56.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:56.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:56.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:56.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:56.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:56.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:56.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:56.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:56.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:56.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:56.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:57.011][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:57.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:57.015][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:57.016][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:57.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:58.108][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:58.139][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.content"
biodb.TRACE[2022-04-12 06:35:58.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.request"
biodb.DEBUG[2022-04-12 06:35:58.209][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[2022-04-12 06:35:58.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:58.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:58.215][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:35:58.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:35:59.229][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:35:59.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.content"
biodb.TRACE[2022-04-12 06:35:59.343][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.request"
biodb.DEBUG[2022-04-12 06:35:59.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:59.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:59.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:59.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:59.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:59.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:35:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:59.446][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 06:35:59.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:59.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.485][private$selectFields]
biodb.TRACE[2022-04-12 06:35:59.486][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:59.487][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:59.488][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.493][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.494][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.495][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.498][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.499][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.502][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.506][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.508][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.509][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:59.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.528][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-04-12 06:35:59.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.551][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.552][private$selectFields]
biodb.TRACE[2022-04-12 06:35:59.553][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:59.555][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:59.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.561][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.562][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.566][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.568][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.569][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.570][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.575][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.576][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.586][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:59.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.606][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 06:35:59.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:35:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.630][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.632][private$selectFields]
biodb.TRACE[2022-04-12 06:35:59.633][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:35:59.634][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:35:59.635][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.640][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.641][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.642][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.644][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.645][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.646][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.649][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:35:59.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.653][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.654][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.656][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:35:59.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:35:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.674][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-04-12 06:35:59.676][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 06:35:59.677][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 06:35:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 06:35:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 06:35:59.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 06:35:59.698][biodb::testThat]
biodb.INFO [2022-04-12 06:35:59.699][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-04-12 06:35:59.700][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:35:59.702][biodb::testThat]
biodb.TRACE[2022-04-12 06:35:59.706][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 06:35:59.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 06:35:59.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:35:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:35:59.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:35:59.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:35:59.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:35:59.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:35:59.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:35:59.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:35:59.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:35:59.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:35:59.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:35:59.897][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:35:59.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:35:59.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:35:59.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:00.357][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:00.918][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:00.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content"
biodb.TRACE[2022-04-12 06:36:00.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.request"
biodb.DEBUG[2022-04-12 06:36:01.017][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[2022-04-12 06:36:01.021][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:01.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:01.025][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:01.505][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:01.994][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:02.013][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content"
biodb.TRACE[2022-04-12 06:36:02.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.request"
biodb.DEBUG[2022-04-12 06:36:02.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:02.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:02.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:02.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:02.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:02.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:02.074][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:02.077][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:02.078][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d57f841033be8ab371045edb0388ed60".
biodb.TRACE[2022-04-12 06:36:02.079][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:02.080][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content".
biodb.DEBUG[2022-04-12 06:36:02.083][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 06:36:02.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.106][private$selectFields]
biodb.TRACE[2022-04-12 06:36:02.107][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:36:02.108][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:36:02.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.111][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.112][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.113][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.114][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.115][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.116][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.117][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.118][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.119][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.121][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.121][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.122][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:36:02.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.135][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 06:36:02.136][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 06:36:02.136][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 06:36:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:02.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:02.318][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:02.322][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:02.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c60f2116f91d4ce61370ae6298305b49".
biodb.TRACE[2022-04-12 06:36:02.325][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:02.326][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.content".
biodb.DEBUG[2022-04-12 06:36:02.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:02.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:02.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "921bb2fccd1f3497458cb7cf8fd2ffda".
biodb.TRACE[2022-04-12 06:36:02.334][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:02.336][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.content".
biodb.DEBUG[2022-04-12 06:36:02.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:02.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:02.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:02.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:02.393][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 06:36:02.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.410][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.410][private$selectFields]
biodb.TRACE[2022-04-12 06:36:02.411][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:36:02.412][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:36:02.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.416][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.417][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.420][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.421][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.422][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.423][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.424][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.425][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.426][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.426][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.427][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:36:02.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.440][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-04-12 06:36:02.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.466][private$selectFields]
biodb.TRACE[2022-04-12 06:36:02.467][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:36:02.468][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:36:02.468][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.469][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.470][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.471][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.472][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.473][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.475][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.476][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.477][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.478][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.481][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.482][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.483][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:36:02.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.497][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 06:36:02.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:02.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.514][private$selectFields]
biodb.TRACE[2022-04-12 06:36:02.515][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 06:36:02.516][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 06:36:02.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.517][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.518][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.519][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.520][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.522][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.523][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.524][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.525][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.526][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 06:36:02.527][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.528][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.529][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.529][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.530][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 06:36:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:02.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:02.543][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-04-12 06:36:02.544][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 06:36:02.545][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 06:36:02.566][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 06:36:02.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 06:36:02.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:02.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 06:36:02.571][biodb::testThat]
biodb.INFO [2022-04-12 06:36:02.572][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2022-04-12 06:36:02.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:02.574][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:02.577][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-04-12 06:36:02.578][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:36:02.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-04-12 06:36:02.581][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:36:02.582][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:36:02.583][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:36:02.584][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:36:02.585][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:36:02.586][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:36:02.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:02.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:02.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:02.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:02.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:02.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:02.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:02.596][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2022-04-12 06:36:02.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:02.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:02.601][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2022-04-12 06:36:03.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2022-04-12 06:36:03.641][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:03.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2022-04-12 06:36:03.702][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2022-04-12 06:36:03.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2022-04-12 06:36:03.746][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:36:03.768][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:36:03.770][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:36:03.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:03.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:03.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:03.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:03.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:03.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:03.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:03.780][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.781][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.782][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.783][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.798][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:03.799][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:03.800][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.801][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.802][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:03.803][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:03.804][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.805][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.806][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:03.807][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:03.808][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.809][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:03.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:03.812][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.812][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.813][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:03.814][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:03.815][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.816][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.817][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:03.818][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:03.819][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.820][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.821][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:03.822][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:03.823][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.824][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.825][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:03.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:03.827][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.828][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.829][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:03.830][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:03.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.832][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.833][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:03.834][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:03.835][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.836][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:03.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:03.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:03.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:03.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:03.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:03.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:03.890][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2022-04-12 06:36:03.891][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.INFO [2022-04-12 06:36:03.897][biodb::testThat]
biodb.INFO [2022-04-12 06:36:03.899][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-04-12 06:36:03.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:03.901][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:03.910][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2022-04-12 06:36:03.911][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2022-04-12 06:36:03.912][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2022-04-12 06:36:03.914][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2022-04-12 06:36:03.915][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2022-04-12 06:36:03.916][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:36:03.917][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:36:03.918][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:36:03.919][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:36:03.920][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:36:03.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:03.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:03.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:03.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:03.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:03.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:03.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:03.930][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2022-04-12 06:36:03.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:03.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:03.936][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2022-04-12 06:36:04.391][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2022-04-12 06:36:04.928][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:04.961][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2022-04-12 06:36:05.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2022-04-12 06:36:05.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:05.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:05.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:05.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:05.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:05.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:05.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:05.048][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2022-04-12 06:36:05.056][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:05.058][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:05.061][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2022-04-12 06:36:05.661][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2022-04-12 06:36:06.255][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:06.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2022-04-12 06:36:06.334][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2022-04-12 06:36:06.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:06.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:06.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:06.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:06.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:06.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:06.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:06.354][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2022-04-12 06:36:06.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:06.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:06.359][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2022-04-12 06:36:06.854][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2022-04-12 06:36:07.401][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:07.431][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2022-04-12 06:36:07.497][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2022-04-12 06:36:07.538][private$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[2022-04-12 06:36:07.550][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:36:07.576][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2022-04-12 06:36:07.578][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2022-04-12 06:36:07.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:07.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:07.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:07.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:07.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:07.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:07.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:07.589][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.590][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.591][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.592][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.609][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:07.611][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:07.612][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.613][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.614][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:07.615][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:07.616][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.617][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.618][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:07.619][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:07.620][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.621][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.622][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:07.623][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:07.624][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.625][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.626][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:07.627][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:07.628][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.629][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.630][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:07.631][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:07.632][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.633][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.634][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:07.635][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:07.636][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.637][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.638][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:07.639][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:07.640][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.641][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.642][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:07.643][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:07.644][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.645][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.646][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:07.647][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:07.648][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.649][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:07.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:07.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:07.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:07.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:07.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:07.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:07.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:07.700][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.701][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.701][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.702][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.716][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:07.718][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:07.719][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.719][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:07.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:07.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.734][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:07.735][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:07.736][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.737][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:07.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.752][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:07.753][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:07.754][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.755][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:07.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:07.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:07.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:07.772][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.773][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:07.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:07.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.788][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:07.789][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:07.790][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.791][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.793][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:07.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:07.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.807][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:07.808][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:07.809][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.810][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.811][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:07.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:07.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.825][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:07.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:07.827][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.828][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:07.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:07.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.844][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:07.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:07.846][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.847][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:07.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:07.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.862][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:07.864][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:07.865][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.866][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.867][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:07.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:07.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.887][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:07.888][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:07.889][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.890][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.892][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:07.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:07.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:07.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:07.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:07.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:07.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:07.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:07.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:07.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:07.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:07.951][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.952][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.953][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.954][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:07.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.970][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:07.971][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:07.972][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.973][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.974][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:07.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:07.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.988][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:07.989][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:07.990][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.991][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:07.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:07.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:07.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:07.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.004][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:08.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:08.007][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.007][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:08.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:08.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.021][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:08.023][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:08.024][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.024][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.026][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:08.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:08.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.038][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:08.039][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:08.040][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.041][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:08.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:08.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.055][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:08.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:08.057][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.058][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.059][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:08.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:08.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.076][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:08.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:08.078][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.079][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:08.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:08.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.093][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:08.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:08.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.096][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:08.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:08.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.109][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:08.110][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:08.111][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.112][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.113][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:08.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:08.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.126][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:08.127][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:08.128][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.129][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.130][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:08.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:08.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:08.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:08.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:08.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:08.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:08.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:08.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:08.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:08.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:08.211][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2022-04-12 06:36:08.212][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.DEBUG[2022-04-12 06:36:08.213][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-04-12 06:36:08.224][biodb::testThat]
biodb.INFO [2022-04-12 06:36:08.225][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2022-04-12 06:36:08.226][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:08.227][biodb::testThat]
biodb.INFO [2022-04-12 06:36:08.253][biodb::testThat]
biodb.INFO [2022-04-12 06:36:08.254][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2022-04-12 06:36:08.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:08.256][biodb::testThat]
biodb.INFO [2022-04-12 06:36:08.262][biodb::testThat]
biodb.INFO [2022-04-12 06:36:08.264][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2022-04-12 06:36:08.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:08.265][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:08.268][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:08.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:08.273][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:08.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:08.789][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:09.488][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:09.512][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/abfdad4f2c265f1c152262cabd0cf864.content"
biodb.TRACE[2022-04-12 06:36:09.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/abfdad4f2c265f1c152262cabd0cf864.request"
biodb.INFO [2022-04-12 06:36:09.564][biodb::testThat]
biodb.INFO [2022-04-12 06:36:09.565][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2022-04-12 06:36:09.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:09.567][biodb::testThat]
biodb.ERROR[2022-04-12 06:36:09.581][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-04-12 06:36:09.595][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-04-12 06:36:09.605][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 06:36:09.607][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 06:36:09.608][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 06:36:09.609][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 06:36:09.610][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:09.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:09.612][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.614][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.614][FUN] Functions in observer BiodbConfig: [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 [2022-04-12 06:36:09.625][biodb::testContext]
biodb.INFO [2022-04-12 06:36:09.626][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:36:09.627][biodb::testContext] Test context - Test conversions
biodb.INFO [2022-04-12 06:36:09.628][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:36:09.629][biodb::testContext]
biodb.INFO [2022-04-12 06:36:09.643][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:36:09.645][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 06:36:09.650][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:09.651][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 06:36:09.652][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 06:36:09.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.656][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 06:36:09.657][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 06:36:09.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.669][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 06:36:09.671][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 06:36:09.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.675][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 06:36:09.676][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 06:36:09.677][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 06:36:09.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.679][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[2022-04-12 06:36:09.680][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 06:36:09.681][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 06:36:09.682][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 06:36:09.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.686][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 06:36:09.687][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 06:36:09.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.690][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[2022-04-12 06:36:09.691][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 06:36:09.692][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 06:36:09.693][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 06:36:09.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.696][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 06:36:09.697][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 06:36:09.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.701][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 06:36:09.702][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 06:36:09.703][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 06:36:09.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.706][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:36:09.707][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 06:36:09.708][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 06:36:09.709][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 06:36:09.710][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 06:36:09.711][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 06:36:09.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.714][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[2022-04-12 06:36:09.714][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 06:36:09.716][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 06:36:09.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.719][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 06:36:09.720][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 06:36:09.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.724][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 06:36:09.725][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 06:36:09.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 06:36:09.729][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 06:36:09.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.732][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 06:36:09.733][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 06:36:09.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.737][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:36:09.738][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 06:36:09.742][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-04-12 06:36:09.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.745][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[2022-04-12 06:36:09.746][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 06:36:09.747][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 06:36:09.748][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 06:36:09.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.752][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 06:36:09.754][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.755][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 06:36:09.756][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.757][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:09.758][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.759][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.760][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.762][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:36:09.763][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:09.764][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.765][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 06:36:09.766][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:09.767][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.768][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.769][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:09.769][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:09.769][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:09.769][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:36:09.769][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:36:09.770][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:09.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.773][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:09.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.776][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.777][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.778][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:09.779][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:09.780][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.781][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.782][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 06:36:09.784][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.785][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:36:09.786][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.787][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:09.788][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.789][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.790][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.791][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.792][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:36:09.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:09.794][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.795][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 06:36:09.796][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:09.797][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.798][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.799][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:09.799][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:09.799][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:09.799][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:36:09.799][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:36:09.800][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:09.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.803][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:09.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.807][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:09.816][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:09.817][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.818][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.820][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 06:36:09.823][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.824][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 06:36:09.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.827][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:09.828][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.830][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.832][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:36:09.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:09.835][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.836][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 06:36:09.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:09.838][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.840][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.841][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.842][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:09.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:09.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.850][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:09.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:09.873][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.876][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.878][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 06:36:09.882][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.883][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:36:09.884][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.885][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:09.886][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.888][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.889][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.890][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.891][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:36:09.892][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:09.893][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.894][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 06:36:09.895][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:09.897][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.898][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:09.899][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.900][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:09.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:09.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:09.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:09.906][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:09.907][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.908][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:09.909][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:09.910][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:09.911][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:09.912][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:09.913][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.914][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[2022-04-12 06:36:09.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.919][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[2022-04-12 06:36:09.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.923][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[2022-04-12 06:36:09.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.938][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.DEBUG[2022-04-12 06:36:09.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.951][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[2022-04-12 06:36:09.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.960][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.DEBUG[2022-04-12 06:36:09.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:09.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:09.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:09.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:09.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:09.996][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 06:36:09.998][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 06:36:10.000][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 06:36:10.002][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 06:36:10.003][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:36:10.005][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 06:36:10.007][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 06:36:10.008][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 06:36:10.010][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 06:36:10.012][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 06:36:10.013][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:36:10.015][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 06:36:10.017][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 06:36:10.019][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 06:36:10.020][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 06:36:10.022][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 06:36:10.024][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 06:36:10.025][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 06:36:10.027][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:36:10.029][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 06:36:10.030][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 06:36:10.032][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 06:36:10.033][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 06:36:10.035][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 06:36:10.036][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 06:36:10.038][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 06:36:10.039][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 06:36:10.041][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 06:36:10.042][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 06:36:10.044][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 06:36:10.045][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 06:36:10.047][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 06:36:10.048][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 06:36:10.049][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 06:36:10.051][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 06:36:10.052][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 06:36:10.054][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 06:36:10.055][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 06:36:10.057][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 06:36:10.058][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 06:36:10.068][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 06:36:10.070][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 06:36:10.072][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 06:36:10.074][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 06:36:10.075][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 06:36:10.077][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 06:36:10.078][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 06:36:10.080][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 06:36:10.081][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 06:36:10.083][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 06:36:10.084][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 06:36:10.086][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 06:36:10.087][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 06:36:10.089][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 06:36:10.090][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 06:36:10.091][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 06:36:10.093][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 06:36:10.094][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 06:36:10.096][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 06:36:10.097][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 06:36:10.098][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 06:36:10.100][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 06:36:10.101][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 06:36:10.102][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 06:36:10.104][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 06:36:10.105][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 06:36:10.106][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:36:10.108][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:36:10.109][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 06:36:10.111][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 06:36:10.112][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 06:36:10.113][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 06:36:10.115][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 06:36:10.116][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 06:36:10.117][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 06:36:10.118][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 06:36:10.120][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 06:36:10.121][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 06:36:10.123][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 06:36:10.124][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 06:36:10.125][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 06:36:10.127][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 06:36:10.128][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 06:36:10.130][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 06:36:10.131][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:36:10.132][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:10.133][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.135][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.136][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[2022-04-12 06:36:10.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.205][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[2022-04-12 06:36:10.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:10.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:10.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:10.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:10.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:10.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:10.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:10.245][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 06:36:10.247][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 06:36:10.249][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:10.250][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 06:36:10.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:10.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:10.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:10.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:10.254][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:10.255][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 06:36:10.256][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 06:36:10.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:10.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:10.259][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 06:36:10.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 06:36:10.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 06:36:10.262][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:10.263][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:10.263][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:10.263][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:10.264][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 06:36:10.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:10.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:10.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:10.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:10.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:10.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:10.270][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:36:10.270][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 06:36:10.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:10.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:10.273][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:10.274][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 06:36:10.274][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 06:36:10.275][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:36:10.276][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:36:10.278][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 06:36:10.279][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:36:10.281][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:36:10.282][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:36:10.285][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 06:36:10.286][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 06:36:10.288][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 06:36:10.289][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 06:36:10.290][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:36:10.291][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:36:10.292][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 06:36:10.293][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 06:36:10.295][biodb::testThat]
biodb.INFO [2022-04-12 06:36:10.296][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2022-04-12 06:36:10.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:10.297][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:10.302][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 06:36:10.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:10.307][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:10.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2022-04-12 06:36:10.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2022-04-12 06:36:11.440][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:11.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2022-04-12 06:36:11.484][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2022-04-12 06:36:11.495][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:11.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:11.499][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:11.501][private$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[2022-04-12 06:36:11.959][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[2022-04-12 06:36:12.447][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:12.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2022-04-12 06:36:12.517][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2022-04-12 06:36:12.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:12.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:12.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:12.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:12.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:12.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:12.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:12.549][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[2022-04-12 06:36:12.560][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:12.561][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:12.563][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:13.017][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:13.543][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:13.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2022-04-12 06:36:13.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2022-04-12 06:36:13.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.665][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:13.668][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:13.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-04-12 06:36:13.670][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:13.671][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-04-12 06:36:13.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.680][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:13.682][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:13.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-04-12 06:36:13.685][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:13.686][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-04-12 06:36:13.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.703][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:13.706][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:13.707][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-04-12 06:36:13.708][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:13.709][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-04-12 06:36:13.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.719][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:13.721][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:13.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-04-12 06:36:13.724][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:13.725][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-04-12 06:36:13.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:13.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:13.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:13.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:13.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:13.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:13.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:13.734][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:13.737][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:13.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:13.740][private$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[2022-04-12 06:36:14.365][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[2022-04-12 06:36:14.940][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:14.976][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2022-04-12 06:36:15.048][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2022-04-12 06:36:15.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:15.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:15.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:15.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:15.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:15.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:15.076][FUN] Functions in observer BiodbConfig: [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 [2022-04-12 06:36:15.081][biodb::testThat]
biodb.INFO [2022-04-12 06:36:15.083][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2022-04-12 06:36:15.084][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:15.085][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:15.088][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[2022-04-12 06:36:15.091][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:15.092][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:15.093][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:15.561][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:16.071][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:16.094][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3d0a94707e73df0ba810a5a87df958c6.content"
biodb.TRACE[2022-04-12 06:36:16.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3d0a94707e73df0ba810a5a87df958c6.request"
biodb.DEBUG[2022-04-12 06:36:16.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:16.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:16.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:16.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:16.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:16.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:16.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:16.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:16.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:16.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:16.179][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:16.749][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:17.326][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:17.346][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c23a09621704f6dcea62f90283def982.content"
biodb.TRACE[2022-04-12 06:36:17.377][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c23a09621704f6dcea62f90283def982.request"
biodb.DEBUG[2022-04-12 06:36:17.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:17.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 06:36:17.398][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 06:36:17.399][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 06:36:17.400][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 06:36:17.401][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 06:36:17.402][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.404][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.406][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.407][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.INFO [2022-04-12 06:36:17.411][biodb::testContext]
biodb.INFO [2022-04-12 06:36:17.412][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:36:17.413][biodb::testContext] Test context - Test web services
biodb.INFO [2022-04-12 06:36:17.414][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:36:17.415][biodb::testContext]
biodb.INFO [2022-04-12 06:36:17.440][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:36:17.442][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 06:36:17.447][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:17.448][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 06:36:17.449][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 06:36:17.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.453][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 06:36:17.454][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 06:36:17.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.457][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 06:36:17.459][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 06:36:17.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.462][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 06:36:17.463][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 06:36:17.464][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 06:36:17.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.468][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 06:36:17.469][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 06:36:17.470][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 06:36:17.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.474][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 06:36:17.475][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 06:36:17.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.479][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 06:36:17.480][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 06:36:17.481][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 06:36:17.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.485][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 06:36:17.486][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 06:36:17.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.490][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[2022-04-12 06:36:17.491][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 06:36:17.492][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 06:36:17.493][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 06:36:17.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.497][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:36:17.498][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 06:36:17.499][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 06:36:17.500][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 06:36:17.501][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 06:36:17.502][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 06:36:17.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.505][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 06:36:17.506][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 06:36:17.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.510][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 06:36:17.511][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 06:36:17.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.514][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[2022-04-12 06:36:17.515][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 06:36:17.516][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 06:36:17.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.519][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 06:36:17.520][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 06:36:17.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.523][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[2022-04-12 06:36:17.524][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 06:36:17.525][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 06:36:17.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.528][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:36:17.529][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 06:36:17.535][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-04-12 06:36:17.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.539][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 06:36:17.540][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 06:36:17.541][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 06:36:17.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.545][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 06:36:17.547][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.548][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 06:36:17.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:17.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.554][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.555][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.556][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:36:17.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:17.558][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.559][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 06:36:17.560][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:17.561][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.562][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.563][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:17.563][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:17.563][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:17.563][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:36:17.563][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:36:17.564][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:17.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:17.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.570][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.571][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:17.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:17.575][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.576][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.577][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 06:36:17.579][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.581][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:36:17.582][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.583][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:17.584][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.585][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.586][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.588][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:36:17.590][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:17.591][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.592][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 06:36:17.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:17.594][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:17.596][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:17.596][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:17.596][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:36:17.596][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:36:17.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:17.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:17.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.604][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:17.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:17.607][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.609][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.634][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 06:36:17.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.639][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 06:36:17.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:17.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.647][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:36:17.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:17.649][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.650][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 06:36:17.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:17.652][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.653][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.654][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.655][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:17.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:17.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.662][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:17.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:17.664][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.665][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.667][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 06:36:17.669][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.670][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:36:17.671][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.672][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:17.673][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.677][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:36:17.678][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:17.679][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.680][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 06:36:17.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:17.681][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:17.683][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.684][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:17.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.687][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:17.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:17.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:17.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:17.691][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:17.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:17.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:17.694][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:17.696][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:17.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.702][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[2022-04-12 06:36:17.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.711][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[2022-04-12 06:36:17.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.716][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[2022-04-12 06:36:17.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.720][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[2022-04-12 06:36:17.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.724][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.DEBUG[2022-04-12 06:36:17.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.732][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[2022-04-12 06:36:17.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.741][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[2022-04-12 06:36:17.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.745][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[2022-04-12 06:36:17.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.763][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[2022-04-12 06:36:17.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.773][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 06:36:17.774][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 06:36:17.776][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 06:36:17.777][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 06:36:17.779][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:36:17.780][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 06:36:17.781][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 06:36:17.783][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 06:36:17.784][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 06:36:17.786][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 06:36:17.787][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:36:17.788][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 06:36:17.790][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 06:36:17.791][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 06:36:17.792][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 06:36:17.794][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 06:36:17.795][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 06:36:17.796][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 06:36:17.798][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:36:17.799][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 06:36:17.800][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 06:36:17.808][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 06:36:17.811][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 06:36:17.813][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 06:36:17.815][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 06:36:17.816][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 06:36:17.817][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 06:36:17.819][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 06:36:17.820][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 06:36:17.822][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 06:36:17.823][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 06:36:17.824][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 06:36:17.826][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 06:36:17.827][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 06:36:17.828][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 06:36:17.830][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 06:36:17.831][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 06:36:17.832][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 06:36:17.834][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 06:36:17.835][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 06:36:17.836][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 06:36:17.838][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 06:36:17.839][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 06:36:17.841][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 06:36:17.842][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 06:36:17.843][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 06:36:17.845][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 06:36:17.846][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 06:36:17.847][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 06:36:17.849][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 06:36:17.850][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 06:36:17.851][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 06:36:17.852][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 06:36:17.854][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 06:36:17.855][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 06:36:17.856][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 06:36:17.858][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 06:36:17.859][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 06:36:17.860][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 06:36:17.861][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 06:36:17.863][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 06:36:17.864][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 06:36:17.865][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 06:36:17.867][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 06:36:17.868][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 06:36:17.869][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 06:36:17.870][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:36:17.872][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:36:17.873][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 06:36:17.874][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 06:36:17.876][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 06:36:17.877][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 06:36:17.878][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 06:36:17.879][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 06:36:17.881][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 06:36:17.882][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 06:36:17.883][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 06:36:17.884][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 06:36:17.886][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 06:36:17.887][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 06:36:17.888][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 06:36:17.890][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 06:36:17.891][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 06:36:17.892][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 06:36:17.894][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:36:17.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:17.896][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.897][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.910][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[2022-04-12 06:36:17.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.940][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[2022-04-12 06:36:17.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.953][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[2022-04-12 06:36:17.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:17.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:17.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:17.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:17.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:17.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:17.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:17.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:18.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:18.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:18.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:18.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:18.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:18.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:18.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:18.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:18.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:18.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:18.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:18.010][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 06:36:18.012][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 06:36:18.014][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:18.015][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 06:36:18.016][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:18.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:18.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:18.019][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:18.020][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:18.021][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 06:36:18.022][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 06:36:18.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:18.024][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:18.025][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 06:36:18.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 06:36:18.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 06:36:18.028][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:18.029][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:18.029][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:18.029][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:18.030][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 06:36:18.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:18.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:18.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:18.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:18.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:18.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:18.036][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:36:18.036][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 06:36:18.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:18.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:18.039][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:18.040][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 06:36:18.040][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 06:36:18.042][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:36:18.043][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:36:18.045][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 06:36:18.046][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:36:18.048][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:36:18.050][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:36:18.053][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 06:36:18.054][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 06:36:18.055][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 06:36:18.057][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 06:36:18.058][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:36:18.059][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:36:18.060][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 06:36:18.061][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 06:36:18.062][biodb::testThat]
biodb.INFO [2022-04-12 06:36:18.063][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2022-04-12 06:36:18.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:18.065][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:18.069][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 06:36:18.072][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:18.074][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 06:36:18.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:18.076][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 06:36:18.080][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[2022-04-12 06:36:18.083][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:18.084][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:18.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 06:36:18.547][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 06:36:19.073][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:19.091][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2022-04-12 06:36:19.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2022-04-12 06:36:19.131][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 06:36:19.133][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 06:36:19.134][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 06:36:19.135][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 06:36:19.136][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.137][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.139][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 06:36:19.144][biodb::testContext]
biodb.INFO [2022-04-12 06:36:19.145][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:36:19.146][biodb::testContext] Test context - Non regression tests
biodb.INFO [2022-04-12 06:36:19.147][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 06:36:19.147][biodb::testContext]
biodb.INFO [2022-04-12 06:36:19.172][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:36:19.173][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 06:36:19.178][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:19.179][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 06:36:19.180][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 06:36:19.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.183][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 06:36:19.184][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 06:36:19.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.187][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 06:36:19.188][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 06:36:19.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.192][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 06:36:19.193][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 06:36:19.193][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 06:36:19.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.197][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 06:36:19.198][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 06:36:19.198][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 06:36:19.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.202][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 06:36:19.203][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 06:36:19.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.206][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 06:36:19.207][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 06:36:19.208][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 06:36:19.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.211][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 06:36:19.212][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 06:36:19.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.215][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 06:36:19.216][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 06:36:19.217][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 06:36:19.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.220][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:36:19.221][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 06:36:19.222][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 06:36:19.222][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 06:36:19.223][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 06:36:19.224][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 06:36:19.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.228][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 06:36:19.228][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 06:36:19.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.232][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 06:36:19.233][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 06:36:19.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.236][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 06:36:19.237][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 06:36:19.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.240][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 06:36:19.241][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 06:36:19.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.244][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 06:36:19.245][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 06:36:19.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.249][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 06:36:19.250][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 06:36:19.255][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-04-12 06:36:19.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.258][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 06:36:19.259][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 06:36:19.260][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 06:36:19.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.264][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 06:36:19.265][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.266][self$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[2022-04-12 06:36:19.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:19.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.271][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.272][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.273][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:36:19.274][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:19.275][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.276][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 06:36:19.277][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:19.278][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.280][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:19.280][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:19.280][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:19.280][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:36:19.280][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:36:19.281][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:19.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:19.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.286][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.287][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.288][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:19.289][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:19.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.291][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.292][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 06:36:19.294][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.295][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:36:19.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.297][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:19.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.301][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:36:19.302][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:19.303][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.304][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 06:36:19.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:19.306][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.307][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.308][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:19.308][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:19.308][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:19.308][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 06:36:19.308][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 06:36:19.309][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:19.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:19.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.316][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:19.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:19.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.319][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.321][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 06:36:19.322][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.323][self$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[2022-04-12 06:36:19.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.325][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:19.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.327][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.337][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 06:36:19.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:19.340][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.341][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 06:36:19.342][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:19.343][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.344][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.345][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.346][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:19.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.348][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:19.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.351][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.352][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:19.354][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:19.355][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.355][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.357][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 06:36:19.358][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.359][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 06:36:19.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.361][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:19.362][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.364][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.366][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 06:36:19.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:19.368][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.369][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 06:36:19.370][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:19.371][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.372][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.373][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.374][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 06:36:19.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:19.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.380][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.381][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:19.382][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:19.383][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.384][self$setPropertyValue]
biodb.DEBUG[2022-04-12 06:36:19.385][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:19.386][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.387][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[2022-04-12 06:36:19.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.416][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[2022-04-12 06:36:19.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.441][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[2022-04-12 06:36:19.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.445][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[2022-04-12 06:36:19.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.458][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 06:36:19.459][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 06:36:19.461][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 06:36:19.462][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 06:36:19.463][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:36:19.465][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 06:36:19.466][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 06:36:19.467][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 06:36:19.468][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 06:36:19.470][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 06:36:19.471][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:36:19.472][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 06:36:19.474][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 06:36:19.475][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 06:36:19.476][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 06:36:19.477][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 06:36:19.479][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 06:36:19.480][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 06:36:19.481][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:36:19.483][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 06:36:19.484][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 06:36:19.485][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 06:36:19.486][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 06:36:19.488][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 06:36:19.494][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 06:36:19.496][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 06:36:19.497][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 06:36:19.499][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 06:36:19.500][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 06:36:19.502][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 06:36:19.503][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 06:36:19.504][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 06:36:19.506][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 06:36:19.507][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 06:36:19.508][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 06:36:19.509][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 06:36:19.511][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 06:36:19.512][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 06:36:19.513][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 06:36:19.514][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 06:36:19.516][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 06:36:19.517][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 06:36:19.518][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 06:36:19.519][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 06:36:19.521][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 06:36:19.522][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 06:36:19.523][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 06:36:19.524][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 06:36:19.526][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 06:36:19.527][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 06:36:19.528][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 06:36:19.529][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 06:36:19.531][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 06:36:19.532][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 06:36:19.533][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 06:36:19.534][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 06:36:19.536][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 06:36:19.537][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 06:36:19.538][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 06:36:19.539][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 06:36:19.540][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 06:36:19.542][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 06:36:19.543][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 06:36:19.544][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 06:36:19.545][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 06:36:19.547][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 06:36:19.548][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:36:19.549][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:36:19.550][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 06:36:19.551][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 06:36:19.553][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 06:36:19.554][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 06:36:19.555][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 06:36:19.556][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 06:36:19.557][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 06:36:19.559][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 06:36:19.560][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 06:36:19.561][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 06:36:19.562][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 06:36:19.564][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 06:36:19.565][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 06:36:19.566][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 06:36:19.567][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 06:36:19.569][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 06:36:19.570][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 06:36:19.571][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 06:36:19.572][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.573][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.658][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[2022-04-12 06:36:19.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 06:36:19.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.677][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.14-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 06:36:19.678][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 06:36:19.680][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.681][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.682][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.683][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 06:36:19.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.685][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.685][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.686][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 06:36:19.687][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 06:36:19.688][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 06:36:19.689][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.690][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 06:36:19.691][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 06:36:19.692][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 06:36:19.693][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 06:36:19.694][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 06:36:19.694][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 06:36:19.694][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 06:36:19.695][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 06:36:19.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.698][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 06:36:19.699][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 06:36:19.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 06:36:19.700][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 06:36:19.701][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:36:19.701][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 06:36:19.702][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 06:36:19.703][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 06:36:19.704][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 06:36:19.705][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 06:36:19.705][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 06:36:19.706][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 06:36:19.708][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 06:36:19.709][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 06:36:19.711][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 06:36:19.712][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 06:36:19.714][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 06:36:19.717][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 06:36:19.718][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 06:36:19.719][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 06:36:19.720][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 06:36:19.721][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:36:19.722][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 06:36:19.724][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 06:36:19.725][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 06:36:19.726][biodb::testThat]
biodb.INFO [2022-04-12 06:36:19.727][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2022-04-12 06:36:19.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 06:36:19.729][biodb::testThat]
biodb.DEBUG[2022-04-12 06:36:19.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 06:36:19.735][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:19.737][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 06:36:19.738][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:19.739][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 06:36:19.743][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 06:36:19.745][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 06:36:19.747][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2022-04-12 06:36:19.748][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 06:36:19.749][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2022-04-12 06:36:19.753][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2022-04-12 06:36:19.754][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 06:36:19.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2022-04-12 06:36:19.756][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 06:36:19.757][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 06:36:19.758][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 06:36:19.759][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 06:36:19.760][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 06:36:19.761][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 06:36:19.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:19.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:19.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:19.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:19.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:19.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:19.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 06:36:19.775][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2022-04-12 06:36:19.778][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 06:36:19.779][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 06:36:19.780][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2022-04-12 06:36:21.199][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2022-04-12 06:36:22.149][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 06:36:22.185][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2022-04-12 06:36:22.237][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2022-04-12 06:36:22.299][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2022-04-12 06:36:22.310][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 06:36:22.332][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 06:36:22.334][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 06:36:22.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 06:36:22.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:22.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:22.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:22.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:22.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:22.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 06:36:22.345][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.346][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.346][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.347][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.362][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:22.364][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:22.365][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.366][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.367][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 06:36:22.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 06:36:22.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.384][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:22.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:22.387][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.388][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.390][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 06:36:22.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 06:36:22.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.410][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 06:36:22.412][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 06:36:22.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.415][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 06:36:22.419][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 06:36:22.420][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.422][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.424][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:22.425][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:22.427][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.428][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.430][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:22.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 06:36:22.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.451][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:22.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:22.454][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.456][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 06:36:22.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 06:36:22.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.486][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:22.489][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:22.490][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.492][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:22.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 06:36:22.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.514][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:22.516][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:22.517][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.518][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 06:36:22.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 06:36:22.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.536][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:22.538][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:22.538][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.539][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.541][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 06:36:22.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 06:36:22.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.554][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:22.555][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:22.556][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.556][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 06:36:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 06:36:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:22.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:22.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:22.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:22.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 06:36:22.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 06:36:22.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 06:36:22.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 06:36:22.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 06:36:22.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 06:36:22.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 06:36:22.617][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2022-04-12 06:36:22.618][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 06:36:22.620][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 06:36:22.621][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 06:36:22.621][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 06:36:22.622][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 06:36:22.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 06:36:22.624][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 06:36:22.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 06:36:22.626][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 06:36:22.626][FUN] Functions in observer 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 356 ]
>
> proc.time()
user system elapsed
27.861 0.787 72.631
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.335 | 0.135 | 3.748 | |
| ChebiEntry | 0.403 | 0.000 | 0.403 | |