Pierrick Roger
| Snapshot Date: 2024-11-01 13:40 -0400 (Fri, 01 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-02 12:07 -0400 (Sat, 02 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4500 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4505 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.12.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2024-11-02 05:20:42 -0000 (Sat, 02 Nov 2024) |
| EndedAt: 2024-11-02 05:25:12 -0000 (Sat, 02 Nov 2024) |
| EllapsedTime: 270.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 1.289 0.032 5.155
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/R/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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 [2024-11-02 05:21:46.977][biodb::testContext]
biodb.INFO [2024-11-02 05:21:46.980][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:21:46.982][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-02 05:21:46.983][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:21:46.985][biodb::testContext]
biodb.INFO [2024-11-02 05:21:46.993][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:21:46.996][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 05:21:47.006][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:21:47.008][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 05:21:47.009][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 05:21:47.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.015][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 05:21:47.044][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 05:21:47.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.049][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 05:21:47.051][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 05:21:47.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.056][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 05:21:47.058][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 05:21:47.059][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 05:21:47.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.066][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[2024-11-02 05:21:47.068][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 05:21:47.069][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 05:21:47.071][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 05:21:47.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.076][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 05:21:47.078][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 05:21:47.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.083][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 05:21:47.085][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 05:21:47.086][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 05:21:47.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.091][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 05:21:47.093][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 05:21:47.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.098][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 05:21:47.100][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 05:21:47.101][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 05:21:47.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.107][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:21:47.108][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 05:21:47.110][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 05:21:47.111][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 05:21:47.113][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 05:21:47.114][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 05:21:47.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.119][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[2024-11-02 05:21:47.120][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 05:21:47.122][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 05:21:47.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.127][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 05:21:47.129][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 05:21:47.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.134][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 05:21:47.136][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 05:21:47.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.141][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 05:21:47.143][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 05:21:47.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.147][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[2024-11-02 05:21:47.149][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 05:21:47.150][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 05:21:47.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.156][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:21:47.158][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 05:21:47.164][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 05:21:47.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.170][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 05:21:47.171][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 05:21:47.173][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 05:21:47.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.182][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 05:21:47.233][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.270][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-02 05:21:47.272][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.273][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:21:47.275][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.276][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.278][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.279][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.280][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:21:47.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:21:47.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.285][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 05:21:47.286][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:21:47.288][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.289][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.291][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:21:47.291][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:21:47.291][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:21:47.291][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:21:47.291][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:21:47.292][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:21:47.294][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.296][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:21:47.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.302][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:21:47.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:21:47.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.307][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.309][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 05:21:47.312][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.313][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:21:47.315][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.316][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:21:47.318][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.319][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.320][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.323][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:21:47.325][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:21:47.326][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.328][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 05:21:47.329][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:21:47.330][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.332][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.333][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:21:47.333][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:21:47.333][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:21:47.333][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:21:47.333][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:21:47.335][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:21:47.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:21:47.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.344][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.345][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:21:47.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:21:47.350][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.351][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.353][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 05:21:47.356][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.357][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-02 05:21:47.359][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:21:47.362][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.365][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.367][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:21:47.369][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:21:47.370][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.372][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 05:21:47.373][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:21:47.375][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.376][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.377][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:21:47.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:21:47.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.387][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.388][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.390][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:21:47.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:21:47.393][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.394][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.396][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 05:21:47.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.400][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:21:47.402][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:21:47.404][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.410][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:21:47.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:21:47.413][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.414][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 05:21:47.416][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:21:47.417][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.419][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:47.420][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.422][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:21:47.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.426][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:21:47.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:47.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:47.430][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:21:47.431][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.432][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:21:47.434][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:21:47.435][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:47.436][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:21:47.442][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:21:47.443][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.457][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[2024-11-02 05:21:47.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.514][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[2024-11-02 05:21:47.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.527][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[2024-11-02 05:21:47.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.540][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[2024-11-02 05:21:47.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.555][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 05:21:47.561][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 05:21:47.564][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 05:21:47.566][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 05:21:47.568][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:21:47.570][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 05:21:47.573][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 05:21:47.575][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 05:21:47.577][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 05:21:47.580][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 05:21:47.582][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:21:47.584][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 05:21:47.587][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 05:21:47.589][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 05:21:47.591][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 05:21:47.594][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 05:21:47.596][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 05:21:47.599][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 05:21:47.601][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:21:47.603][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 05:21:47.606][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 05:21:47.608][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 05:21:47.610][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 05:21:47.612][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 05:21:47.614][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 05:21:47.616][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 05:21:47.618][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 05:21:47.621][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 05:21:47.623][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 05:21:47.625][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 05:21:47.627][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 05:21:47.629][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 05:21:47.631][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 05:21:47.633][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 05:21:47.635][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 05:21:47.637][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 05:21:47.639][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 05:21:47.649][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 05:21:47.652][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 05:21:47.654][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 05:21:47.656][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 05:21:47.659][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 05:21:47.661][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 05:21:47.663][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 05:21:47.665][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 05:21:47.668][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 05:21:47.670][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 05:21:47.684][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 05:21:47.687][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 05:21:47.689][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 05:21:47.691][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 05:21:47.693][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 05:21:47.712][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 05:21:47.714][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 05:21:47.716][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 05:21:47.719][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 05:21:47.721][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 05:21:47.724][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 05:21:47.726][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 05:21:47.739][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 05:21:47.742][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 05:21:47.744][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 05:21:47.747][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 05:21:47.749][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 05:21:47.766][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 05:21:47.768][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 05:21:47.771][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:21:47.774][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:21:47.776][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 05:21:47.778][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 05:21:47.797][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 05:21:47.799][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 05:21:47.801][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 05:21:47.804][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 05:21:47.806][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 05:21:47.808][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 05:21:47.810][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 05:21:47.828][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 05:21:47.831][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 05:21:47.833][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 05:21:47.835][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 05:21:47.837][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 05:21:47.839][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 05:21:47.863][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 05:21:47.866][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:21:47.870][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:21:47.872][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:47.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:47.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:47.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:47.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:47.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:47.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:47.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:47.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.965][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[2024-11-02 05:21:47.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:47.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:47.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:47.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:47.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:47.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:47.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:47.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:47.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:47.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.009][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[2024-11-02 05:21:48.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.085][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[2024-11-02 05:21:48.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:21:48.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.191][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[2024-11-02 05:21:48.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:21:48.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.200][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[2024-11-02 05:21:48.202][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-02 05:21:48.233][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-02 05:21:48.253][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:48.254][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 05:21:48.256][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:48.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:21:48.259][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:48.261][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:21:48.263][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:48.264][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-02 05:21:48.266][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 05:21:48.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:21:48.293][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:48.295][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-02 05:21:48.296][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-02 05:21:48.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-02 05:21:48.300][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 05:21:48.301][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:21:48.301][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:21:48.301][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:21:48.303][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 05:21:48.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:48.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:48.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:21:48.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:21:48.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:21:48.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:21:48.322][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:21:48.322][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-02 05:21:48.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:21:48.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:21:48.326][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 05:21:48.327][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-02 05:21:48.327][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-02 05:21:48.354][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:21:48.356][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:21:48.359][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-02 05:21:48.361][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:21:48.377][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:21:48.379][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:21:48.453][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-02 05:21:48.472][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-02 05:21:48.477][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-02 05:21:48.483][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-02 05:21:48.502][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:21:48.504][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:21:48.506][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-02 05:21:48.507][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-02 05:21:48.536][biodb::testThat]
biodb.INFO [2024-11-02 05:21:48.537][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-02 05:21:48.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:48.540][biodb::testThat]
biodb.TRACE[2024-11-02 05:21:48.583][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-11-02 05:21:48.586][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:21:48.591][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:21:48.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:21:48.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:48.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:48.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:48.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:48.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:48.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:21:48.728][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:48.730][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:48.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.734][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:48.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:48.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.795][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:48.797][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:48.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.805][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.846][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:48.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:48.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.852][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:48.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:48.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.857][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:48.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:48.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.865][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:48.866][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:48.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.869][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:48.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:48.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.877][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:48.879][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:48.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.881][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:48.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:48.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.889][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:48.891][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:48.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.894][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.896][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:48.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:48.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.902][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:21:48.903][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:48.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.906][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.908][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:21:48.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:48.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.914][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:48.916][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:48.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.918][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:48.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:48.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.927][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:48.928][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:48.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.931][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:48.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:48.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.940][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:21:48.941][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:48.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.944][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.946][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:21:48.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:48.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.953][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:48.954][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:48.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.957][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:48.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:48.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:48.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:48.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:48.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:48.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:48.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:48.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:48.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:48.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:48.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:48.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:48.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:48.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:21:49.091][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-02 05:21:49.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:49.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:49.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:49.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:49.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:49.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:49.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:49.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 05:21:49.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 05:21:49.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.175][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 05:21:49.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 05:21:49.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 05:21:49.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 05:21:49.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 05:21:49.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 05:21:49.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.362][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.364][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.367][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:49.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:49.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.566][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.568][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:49.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:49.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:49.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:49.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:49.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:49.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:49.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.655][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:49.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:49.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.659][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:49.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:49.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:49.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:49.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:49.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.722][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:49.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.728][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:49.730][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:49.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.749][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.751][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:49.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:49.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.823][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.828][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:49.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.891][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.912][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:49.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:49.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:49.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.975][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:49.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:49.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.981][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:49.983][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:49.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:49.986][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:49.987][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:50.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.021][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.044][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.050][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.072][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.074][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.077][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.078][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.111][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.118][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.140][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.146][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.148][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.167][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.169][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.246][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.264][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.268][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.270][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.339][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.340][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.359][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.428][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.429][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.432][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.450][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.451][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.454][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.461][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:50.462][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:50.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.465][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.472][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:50.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:50.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.483][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.484][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.494][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.495][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.498][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.504][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.506][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.509][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.515][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:50.517][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:50.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.519][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.526][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:50.528][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:50.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.530][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.537][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.538][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.541][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:50.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:50.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.552][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.558][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.560][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.563][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 05:21:50.573][biodb::testThat]
biodb.INFO [2024-11-02 05:21:50.575][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-02 05:21:50.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:50.578][biodb::testThat]
biodb.DEBUG[2024-11-02 05:21:50.613][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-02 05:21:50.626][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:21:50.635][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-02 05:21:50.637][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:21:50.640][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-02 05:21:50.642][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:21:50.683][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:21:50.706][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:21:50.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:21:50.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:21:50.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:21:50.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:21:50.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:21:50.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:21:50.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:21:50.728][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.730][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.733][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.768][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:50.770][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:50.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.775][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:21:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:21:50.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.781][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:50.783][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:50.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.786][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:21:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:21:50.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.794][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.795][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.798][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:50.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.807][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.809][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.813][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:50.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.823][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.824][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.827][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.829][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:21:50.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.835][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:21:50.837][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:50.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.840][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:21:50.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:50.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.848][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:50.850][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:50.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.852][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:50.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.861][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:50.862][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:50.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:50.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.874][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:21:50.875][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.894][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:21:50.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:21:50.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.900][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.902][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.904][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:21:50.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:21:50.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:50.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:50.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:50.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:50.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:21:50.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:21:50.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:21:50.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:21:50.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:21:50.986][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-02 05:21:50.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-02 05:21:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-02 05:21:50.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:50.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-02 05:21:50.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-02 05:21:50.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:50.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:51.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-02 05:21:51.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-02 05:21:51.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:51.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 05:21:51.017][biodb::testThat]
biodb.INFO [2024-11-02 05:21:51.018][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-02 05:21:51.020][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:51.022][biodb::testThat]
biodb.TRACE[2024-11-02 05:21:51.026][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:51.028][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:51.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:51.032][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:21:51.033][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-02 05:21:51.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:51.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:51.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:51.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:51.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:51.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:51.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:51.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:51.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:51.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:21:51.120][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-02 05:21:51.127][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-02 05:21:51.158][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:21:51.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-02 05:21:51.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:21:51.185][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-02 05:21:51.260][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[2024-11-02 05:21:51.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:21:51.266][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:21:51.268][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:21:53.770][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:21:54.680][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:21:54.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-02 05:21:54.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-02 05:21:54.742][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-02 05:21:54.776][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:54.778][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:21:54.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:54.781][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:54.782][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:54.784][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:54.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:54.803][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 05:21:54.809][biodb::testThat]
biodb.INFO [2024-11-02 05:21:54.811][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-02 05:21:54.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:54.814][biodb::testThat]
biodb.TRACE[2024-11-02 05:21:54.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:54.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:54.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:54.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:54.904][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:54.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:54.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:54.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:21:54.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:21:54.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:21:55.095][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:21:55.100][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:21:55.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-02 05:21:55.104][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:21:55.107][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-02 05:21:55.162][biodb::testThat]
biodb.INFO [2024-11-02 05:21:55.163][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-02 05:21:55.165][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:55.166][biodb::testThat]
biodb.TRACE[2024-11-02 05:21:55.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:55.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:55.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:55.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:55.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.359][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.366][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 05:21:55.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 05:21:55.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 05:21:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 05:21:55.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:55.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:21:55.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:21:55.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:21:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:21:55.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.585][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 05:21:55.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 05:21:55.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 05:21:55.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:21:55.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 05:21:55.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 05:21:55.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:21:55.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 05:21:55.642][biodb::testThat]
biodb.INFO [2024-11-02 05:21:55.660][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-02 05:21:55.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:55.664][biodb::testThat]
biodb.INFO [2024-11-02 05:21:55.701][biodb::testThat]
biodb.INFO [2024-11-02 05:21:55.702][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-02 05:21:55.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:55.706][biodb::testThat]
biodb.INFO [2024-11-02 05:21:55.735][biodb::testThat]
biodb.INFO [2024-11-02 05:21:55.737][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-02 05:21:55.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:55.740][biodb::testThat]
biodb.DEBUG[2024-11-02 05:21:55.752][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-02 05:21:56.627][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-02 05:21:58.609][biodb::testThat]
biodb.INFO [2024-11-02 05:21:58.611][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-02 05:21:58.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:21:58.614][biodb::testThat]
biodb.DEBUG[2024-11-02 05:22:00.764][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-11-02 05:22:01.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:01.588][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:01.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:01.592][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:01.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:01.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:01.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:01.611][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 05:22:01.619][biodb::testThat]
biodb.INFO [2024-11-02 05:22:01.728][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-02 05:22:01.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:22:01.733][biodb::testThat]
biodb.TRACE[2024-11-02 05:22:01.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:01.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:01.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:01.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:01.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:01.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:01.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:01.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:01.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:01.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:01.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:02.030][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:22:02.069][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:22:02.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-02 05:22:02.073][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:22:02.085][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-02 05:22:02.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:22:02.292][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:22:02.307][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-02 05:22:02.309][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:22:02.311][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-11-02 05:22:02.340][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 05:22:02.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 05:22:02.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:02.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:02.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:02.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:02.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:02.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:02.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:02.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:02.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:02.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:02.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:02.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:02.392][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:22:02.417][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:02.418][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:02.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:22:03.152][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:22:03.897][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:03.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-02 05:22:03.906][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-02 05:22:03.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:03.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:03.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:03.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:03.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:03.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:03.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:03.945][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-02 05:22:04.129][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:22:04.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-02 05:22:04.137][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:22:04.258][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:22:04.260][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:22:04.262][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:22:04.264][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:22:04.265][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:22:04.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:04.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:04.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:04.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:04.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:04.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:04.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:04.321][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-02 05:22:04.326][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:04.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:04.330][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-02 05:22:05.086][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-02 05:22:05.825][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:05.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-02 05:22:05.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-02 05:22:05.936][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-02 05:22:05.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:22:05.940][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:22:05.942][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:22:05.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:05.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:05.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:05.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:05.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:05.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:05.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:22:05.962][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:05.964][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:05.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:05.966][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:05.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:05.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:05.975][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:05.976][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:05.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:05.979][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:05.981][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:05.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:05.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:05.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:05.988][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:05.989][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:05.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:05.992][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:05.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:06.003][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:06.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.006][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:06.016][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:06.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.019][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:06.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:06.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.028][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:06.029][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:06.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.032][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.034][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:06.036][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.039][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:06.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.047][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:06.049][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:06.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.052][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:06.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:06.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.060][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:06.062][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:06.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.064][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:06.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:06.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.073][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:06.075][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:06.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.078][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.079][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:06.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:06.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.086][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:06.087][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:06.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.090][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.092][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:06.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:06.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:06.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:06.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:06.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:06.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:06.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:06.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:06.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:06.174][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-02 05:22:06.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:06.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:06.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:06.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:06.207][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[2024-11-02 05:22:06.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:06.213][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:06.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:22:10.886][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:22:12.654][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:12.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-02 05:22:12.669][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-02 05:22:12.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:12.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:12.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:12.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:12.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:12.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:12.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:22:12.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:12.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:12.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:12.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:12.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:12.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:12.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:12.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:12.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:12.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:12.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:12.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:12.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:12.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:12.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:12.915][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-02 05:22:12.917][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:22:12.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-02 05:22:12.922][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:22:12.924][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:22:12.926][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:22:12.944][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:22:12.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:22:12.948][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:22:12.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:12.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:12.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:13.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:13.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:13.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:13.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:13.028][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-02 05:22:13.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:13.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:13.053][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-02 05:22:13.821][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-02 05:22:14.596][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:14.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-02 05:22:14.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-02 05:22:14.609][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-02 05:22:14.611][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:22:14.613][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:22:14.617][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:22:14.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:14.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:14.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:14.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:14.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:14.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:14.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:22:14.639][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.644][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.653][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:14.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:14.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.685][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.688][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:14.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:14.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.695][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:14.697][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:14.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.700][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:14.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:14.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:14.711][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:14.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.714][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:14.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:14.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.722][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:14.724][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:14.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:14.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:14.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.735][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:14.736][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:14.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.739][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.741][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:14.743][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.745][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.747][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:14.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:14.755][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:14.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.758][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:14.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:14.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.766][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:14.767][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:14.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.770][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:14.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:14.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.778][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:14.779][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:14.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.782][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.789][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:14.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:14.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.797][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:14.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:14.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.804][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:14.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:14.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:14.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:14.893][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-02 05:22:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:14.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:14.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:14.943][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:22:15.008][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:22:15.031][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-02 05:22:15.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:22:15.145][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-02 05:22:17.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:17.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:17.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:17.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:17.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:17.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:17.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:22:17.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:17.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:17.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:17.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:17.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:17.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:17.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:17.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:17.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:17.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:17.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:17.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:17.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:17.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:17.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:17.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:17.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:17.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:17.707][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-02 05:22:17.708][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:22:17.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-02 05:22:17.773][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:22:17.775][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:22:17.776][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:22:17.778][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:22:17.780][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:22:17.781][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:22:17.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:17.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:17.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:17.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:17.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:17.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:17.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:17.808][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-02 05:22:17.842][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:17.844][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:17.852][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-02 05:22:22.685][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-02 05:22:28.605][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:28.613][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-02 05:22:28.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-02 05:22:28.626][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-02 05:22:28.632][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:22:28.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:22:28.636][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:22:28.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:28.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:28.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:28.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:28.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:28.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:28.661][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[2024-11-02 05:22:28.684][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.689][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.696][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:28.698][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:28.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.700][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.702][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:28.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:28.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.707][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:28.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:28.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.713][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:28.717][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:28.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.719][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.721][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:28.723][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:28.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.725][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.727][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:28.729][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.732][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.734][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:28.735][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:28.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.738][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.740][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:28.742][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:28.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.744][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:28.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:28.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.753][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:28.754][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:28.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.757][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.759][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:28.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.765][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:28.766][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:28.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.769][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:28.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:28.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:28.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:28.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:28.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:28.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:28.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:28.831][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-02 05:22:28.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:28.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:28.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:28.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:28.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:28.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:28.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:28.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:28.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:28.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:28.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:28.914][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-02 05:22:28.916][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:22:29.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-02 05:22:29.014][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:22:29.190][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:22:32.928][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:22:33.702][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:22:33.704][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:22:33.705][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:22:33.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:33.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:33.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:33.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:33.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:33.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:33.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:33.735][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.INFO [2024-11-02 05:22:33.768][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-11-02 05:22:33.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:33.772][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:33.774][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-02 05:22:36.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-02 05:22:37.247][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:37.251][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-02 05:22:37.256][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-02 05:22:37.260][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-02 05:22:37.262][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:22:37.264][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:22:37.266][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:22:37.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:37.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:37.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:37.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:37.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:37.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:37.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:22:37.288][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.290][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.292][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.300][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:37.302][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:37.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.305][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.307][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:37.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:37.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.311][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.313][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:37.315][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:37.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.317][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:37.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:37.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.324][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.325][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:37.327][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:37.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.330][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.331][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:37.333][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.336][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.338][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:37.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:37.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.342][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.344][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:37.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:37.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.349][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:37.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:37.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.359][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:37.361][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:37.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.364][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.366][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.373][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:37.376][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:37.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.379][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:37.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:37.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:37.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:37.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:37.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:37.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:37.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:37.507][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-02 05:22:37.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:37.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:37.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:37.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:37.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:37.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:37.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:37.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:37.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:37.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:37.557][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-02 05:22:37.559][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:22:37.562][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-02 05:22:37.564][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:22:37.565][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:22:37.567][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:22:37.569][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:22:37.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:22:37.572][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:22:37.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:37.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:37.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:37.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:37.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:37.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:37.590][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[2024-11-02 05:22:37.592][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-02 05:22:37.596][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:37.597][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:37.599][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-02 05:22:38.344][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-02 05:22:41.900][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:22:41.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-02 05:22:41.917][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-02 05:22:41.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-02 05:22:41.926][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:22:41.928][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:22:41.929][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:22:41.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:41.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:41.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:41.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:41.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:41.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:41.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:22:41.960][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:41.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:41.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:41.965][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:41.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:41.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:41.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:41.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:41.972][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:41.974][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:41.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:41.977][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.012][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:42.013][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:42.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.016][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.018][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:42.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:42.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.022][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:42.025][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:42.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.028][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.030][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:42.031][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:42.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.034][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.035][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:42.037][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:42.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.040][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.041][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:42.043][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:22:42.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.045][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.047][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:42.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:42.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.051][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.059][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:22:42.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:22:42.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.065][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:42.066][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:42.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.069][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.070][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:22:42.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:22:42.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.076][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:22:42.078][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:22:42.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.080][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:42.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:42.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:42.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:42.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:42.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:22:42.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:22:42.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:42.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:42.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:42.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:42.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:44.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:44.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:44.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:44.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:44.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:44.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:44.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:44.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:44.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:44.728][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-02 05:22:44.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:44.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:44.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:44.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:22:44.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:44.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:44.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:44.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:44.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:44.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:44.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:22:44.792][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-02 05:22:44.793][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:22:44.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-02 05:22:44.798][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:22:44.816][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:22:44.818][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:22:44.820][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:22:44.821][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:22:44.823][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:22:44.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:44.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:44.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:44.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:44.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:44.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:44.857][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[2024-11-02 05:22:44.859][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-02 05:22:44.879][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:22:44.881][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:22:44.883][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-02 05:22:48.051][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-02 05:22:52.198][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-11-02 05:22:53.553][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-02 05:22:53.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-02 05:22:54.554][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-02 05:22:54.615][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-02 05:22:54.617][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:22:54.619][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:22:54.621][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:22:54.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:22:54.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:22:54.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:22:54.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:22:54.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:22:54.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:22:54.664][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.TRACE[2024-11-02 05:22:57.660][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:57.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:57.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:22:57.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:22:57.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.753][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:57.755][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:57.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.758][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.773][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:22:57.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:22:57.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.779][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:57.780][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:57.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.783][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:22:57.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:22:57.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:57.794][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:57.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:22:57.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:22:57.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.804][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:57.806][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:57.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.809][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:22:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:22:57.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.820][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:57.822][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:57.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.825][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.836][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:57.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:22:57.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.842][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:57.843][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:57.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:22:57.846][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:22:57.862][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:22:57.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:22:57.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.555][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:01.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:01.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.560][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:01.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:01.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.589][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:01.590][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:01.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:01.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.676][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:01.678][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:01.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.683][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.685][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:01.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:01.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.692][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:01.694][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:01.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.699][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.701][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:01.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:01.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:01.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:01.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:01.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:01.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:01.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:01.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:01.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:01.795][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-02 05:23:01.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:01.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:01.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:01.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:01.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:01.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:01.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:01.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:01.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:01.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:01.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:01.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:01.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:01.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:01.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:01.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:01.851][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-02 05:23:01.853][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:23:01.894][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-02 05:23:01.896][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:23:01.898][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:23:01.899][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:23:01.901][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:23:01.903][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:23:01.904][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:23:01.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:01.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:01.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:01.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:01.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:01.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:01.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:01.949][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-02 05:23:01.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:23:01.955][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:23:01.958][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-02 05:23:09.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-02 05:23:12.480][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:23:12.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-02 05:23:12.532][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-02 05:23:12.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-02 05:23:12.539][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:23:12.541][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:23:12.543][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:23:12.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:12.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:12.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:12.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:12.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:12.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:12.580][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.TRACE[2024-11-02 05:23:18.848][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:18.871][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:18.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:18.874][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:19.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:19.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.559][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:19.561][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:19.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.564][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:19.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:19.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.573][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:19.576][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:19.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.582][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:19.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:19.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.591][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:19.592][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:19.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.595][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:19.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:19.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:19.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:19.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:21.528][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:21.533][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:21.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:21.537][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:21.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:21.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:21.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:21.561][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:21.577][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:21.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:21.580][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:21.582][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:21.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:21.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:21.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:21.597][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:21.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:21.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:21.602][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.082][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:23.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.103][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:23.104][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:23.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.107][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.127][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:23.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:23.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.131][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:23.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:23.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.139][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:23.141][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:23.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.143][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.145][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:23.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:23.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.151][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:23.153][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:23.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.155][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:23.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:23.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:23.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:23.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:23.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:23.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:23.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:23.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:23.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:23.229][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-02 05:23:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:23.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:23.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:23.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:23.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:23.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:23.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:23.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:23.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:23.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:23.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:23.276][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-02 05:23:23.278][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:23:23.280][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-02 05:23:23.282][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:23:23.283][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:23:23.285][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:23:23.286][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:23:23.288][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:23:23.289][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:23:23.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:23.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:23.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:23.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:23.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:23.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:23.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:23.312][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-02 05:23:23.318][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:23:23.319][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:23:23.324][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-02 05:23:32.412][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-02 05:23:34.980][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:23:35.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-02 05:23:35.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-02 05:23:35.067][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-02 05:23:35.069][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:23:35.071][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:23:35.073][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:23:35.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:35.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:35.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:35.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:35.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:35.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:35.192][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[2024-11-02 05:23:35.233][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.235][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.238][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.260][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:35.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:35.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.265][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.292][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:35.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:35.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.298][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:35.300][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:35.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.303][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:35.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:35.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.311][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:35.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:35.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.316][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:35.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:35.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:35.329][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:35.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:35.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:35.342][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:35.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.345][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.347][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:35.349][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.352][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.354][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:35.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.367][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:35.369][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:35.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.379][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:35.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:35.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.384][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.395][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:35.397][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:35.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.400][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.402][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:35.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.410][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:35.412][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:35.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.414][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.416][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:35.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:35.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:35.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:35.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:35.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:35.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:35.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:35.483][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-02 05:23:35.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:35.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:35.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:35.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:35.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:35.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:35.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:35.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:35.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:35.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:35.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:35.555][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-02 05:23:35.556][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:23:35.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-02 05:23:35.561][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:23:35.562][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:23:35.568][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:23:35.570][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:23:35.571][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:23:35.573][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:23:35.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:35.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:35.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:35.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:35.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:35.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:35.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:35.603][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-02 05:23:35.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:23:35.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:23:35.613][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-02 05:23:36.343][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-02 05:23:39.558][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:23:39.742][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-02 05:23:39.749][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-02 05:23:39.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-02 05:23:39.758][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:23:39.761][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:23:39.763][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:23:39.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:39.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:39.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:39.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:39.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:39.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:39.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:23:39.798][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.800][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.803][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.810][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:39.812][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:39.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.814][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.817][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:39.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:39.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.822][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:39.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:39.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.826][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:39.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.833][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:39.835][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:39.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.837][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:39.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:39.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.845][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:39.847][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:39.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.849][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:39.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:39.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.856][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:39.858][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:39.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.860][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.863][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:39.864][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:39.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.867][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.869][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:39.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:39.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.874][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:39.876][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:39.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.878][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:39.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:39.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.886][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:39.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:39.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.890][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:39.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.900][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:39.902][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:39.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.905][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:39.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:39.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.913][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:39.915][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:39.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.917][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:39.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:39.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:39.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:39.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:39.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:39.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:39.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:39.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:39.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:39.987][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-02 05:23:39.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:39.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:39.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:39.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:39.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:39.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:39.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:41.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:41.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:41.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:41.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:41.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:41.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:41.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:41.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:41.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:41.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:41.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:41.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:41.736][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-02 05:23:41.737][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:23:41.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-02 05:23:41.827][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:23:41.829][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:23:41.831][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:23:41.833][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:23:41.835][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:23:41.837][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:23:41.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:41.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:41.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:41.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:41.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:41.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:41.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:41.873][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-02 05:23:41.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:23:41.944][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:23:41.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-02 05:23:49.708][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-02 05:23:53.552][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:23:53.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-02 05:23:53.604][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-02 05:23:53.608][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-02 05:23:53.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:23:53.612][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:23:53.614][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:23:53.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:53.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:53.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:53.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:53.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:53.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:53.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:23:53.651][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.653][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.656][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.665][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:53.667][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:53.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.670][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:53.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.678][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:53.679][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:53.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.682][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.684][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:53.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.691][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:53.693][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:53.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.696][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:53.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:53.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.704][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:53.705][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:53.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.708][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:53.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.716][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:53.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:53.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.721][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.723][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:53.725][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.727][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.729][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:53.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.736][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:53.737][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:53.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.740][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:53.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.749][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:53.750][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:53.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.753][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:53.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.761][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:53.763][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:53.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.766][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.768][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:53.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.774][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:53.776][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:53.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.779][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:53.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:53.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:53.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:53.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:53.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:53.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:53.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:53.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:53.876][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-02 05:23:53.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:53.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:53.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:53.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:53.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:53.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:53.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:53.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:53.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:53.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:53.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:53.918][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-02 05:23:53.920][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:23:53.922][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-02 05:23:53.925][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:23:53.926][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:23:53.928][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:23:53.930][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:23:53.932][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:23:53.933][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:23:53.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:53.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:53.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:53.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:53.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:53.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:53.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:53.955][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-11-02 05:23:53.959][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:23:53.961][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:23:53.965][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-11-02 05:23:55.203][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-11-02 05:23:59.280][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:23:59.286][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-11-02 05:23:59.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-11-02 05:23:59.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-11-02 05:23:59.297][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:23:59.299][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:23:59.301][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:23:59.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:59.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:59.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:59.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:59.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:59.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:59.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:23:59.327][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.329][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.340][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:59.341][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:59.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.344][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.346][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:23:59.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:23:59.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.352][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:59.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:59.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:23:59.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:23:59.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.366][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:59.367][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:59.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.370][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:23:59.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:23:59.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.378][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:59.380][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:59.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.382][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:23:59.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:23:59.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.390][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:59.392][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:23:59.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.394][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.396][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:59.398][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.401][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.403][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:23:59.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.409][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:59.410][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:59.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.413][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:59.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:23:59.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.421][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:59.423][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:59.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.426][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:23:59.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:23:59.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.495][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:59.497][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:59.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.500][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.501][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:23:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:23:59.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.508][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:59.509][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:59.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:23:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:23:59.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:59.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:23:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:23:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:23:59.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:23:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:59.578][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-02 05:23:59.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:23:59.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:23:59.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:23:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:23:59.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:59.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:59.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:59.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:59.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:59.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:59.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:59.611][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-02 05:23:59.612][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:23:59.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-11-02 05:23:59.616][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:23:59.618][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:23:59.619][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:23:59.621][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:23:59.622][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:23:59.623][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:23:59.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:23:59.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:23:59.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:23:59.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:23:59.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:23:59.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:23:59.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:23:59.642][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-11-02 05:23:59.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:23:59.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:23:59.650][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-11-02 05:24:00.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-11-02 05:24:01.162][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:01.165][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-11-02 05:24:01.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-11-02 05:24:01.173][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-11-02 05:24:01.199][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:01.201][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:01.203][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:01.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:01.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:01.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:01.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:01.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:01.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:01.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:01.233][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.235][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.261][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:01.263][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:01.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.265][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.267][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:01.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:01.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.272][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:01.273][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:01.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.276][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.278][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:01.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:01.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.283][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:01.284][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:01.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.287][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:01.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.298][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:01.300][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:01.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.302][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:01.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:01.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.323][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:01.325][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:01.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.328][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.329][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:01.331][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.333][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.335][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:01.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:01.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:01.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.345][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:01.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:01.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.353][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:01.354][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:01.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:01.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.364][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:01.366][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:01.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.369][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.370][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:01.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:01.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.376][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:01.378][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:01.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.382][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:01.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:01.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:01.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:01.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:01.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:01.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:01.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:01.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:01.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:01.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:01.447][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-02 05:24:01.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:01.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:01.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:01.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:01.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:01.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:01.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:01.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:01.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:01.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:01.479][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-02 05:24:01.481][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:01.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-02 05:24:01.485][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:01.486][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:01.487][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:01.489][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:01.490][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:01.492][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:01.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:01.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:01.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:01.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:01.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:01.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:01.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:01.510][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-11-02 05:24:01.514][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:01.515][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:01.517][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-11-02 05:24:02.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-11-02 05:24:02.979][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:02.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-11-02 05:24:02.987][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-11-02 05:24:02.990][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-11-02 05:24:02.992][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:02.994][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:02.996][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:02.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:02.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:03.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:03.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:03.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:03.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:03.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:03.014][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.039][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:03.041][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:03.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.043][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.045][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:03.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:03.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.051][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:03.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:03.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.055][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.057][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:03.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:03.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.062][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:03.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:03.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.067][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.068][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:03.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:03.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.072][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.075][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:03.077][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:03.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.080][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.082][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:03.083][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.086][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.088][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:03.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:03.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:03.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.098][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:03.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:03.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.106][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:03.108][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:03.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.111][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:03.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:03.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.118][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:03.120][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:03.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.123][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.124][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:03.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:03.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.130][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:03.132][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:03.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.135][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:03.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:03.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:03.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:03.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:03.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:03.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:03.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:03.197][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-02 05:24:03.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:03.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:03.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:03.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:03.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:03.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:03.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:03.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:03.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:03.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:03.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:03.228][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-02 05:24:03.230][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:03.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-02 05:24:03.234][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:03.236][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:03.238][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:03.239][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:03.241][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:03.242][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:03.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:03.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:03.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:03.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:03.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:03.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:03.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:03.261][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-11-02 05:24:03.265][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:03.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:03.269][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-11-02 05:24:05.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-11-02 05:24:05.728][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:05.731][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-11-02 05:24:05.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-11-02 05:24:05.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-11-02 05:24:05.740][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:05.742][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:05.743][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:05.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:05.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:05.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:05.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:05.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:05.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:05.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:05.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.777][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.779][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.787][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:05.788][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:05.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.791][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.792][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:05.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:05.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.798][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:05.799][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:05.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:05.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:05.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.809][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:05.811][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:05.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.813][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.815][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:05.816][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:05.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.819][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.821][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:05.822][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:05.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.825][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.826][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:05.828][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.830][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.832][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:05.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.838][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:05.839][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:05.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.841][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:05.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:05.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.849][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:05.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:05.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.853][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:05.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:05.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.860][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:05.862][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:05.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.864][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.866][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:05.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:05.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.871][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:05.873][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:05.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.875][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:05.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:05.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:05.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:05.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:05.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:05.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:05.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:05.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:05.931][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-02 05:24:05.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:05.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:05.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:05.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:05.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:05.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:05.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:05.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:05.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:05.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:05.963][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-02 05:24:05.964][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:05.966][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-11-02 05:24:05.968][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:05.970][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:05.971][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:05.972][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:05.974][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:05.975][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:05.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:05.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:05.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:05.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:05.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:05.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:05.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:05.993][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-11-02 05:24:06.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:06.007][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:06.009][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-11-02 05:24:06.736][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-11-02 05:24:07.467][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:07.470][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-11-02 05:24:07.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-11-02 05:24:07.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-11-02 05:24:07.482][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:07.484][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:07.486][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:07.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:07.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:07.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:07.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:07.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:07.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:07.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:07.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.507][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.510][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.517][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:07.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:07.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.522][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:07.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:07.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.529][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:07.531][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:07.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.546][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:07.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:07.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.554][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:07.556][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:07.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.558][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:07.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:07.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.566][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:07.568][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:07.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.570][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:07.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:07.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.578][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:07.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:07.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.582][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.584][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:07.586][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.589][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.591][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:07.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.597][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:07.599][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:07.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.601][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:07.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:07.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.609][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:07.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:07.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.613][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:07.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:07.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.621][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:07.623][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:07.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.626][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.628][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:07.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:07.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.633][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:07.635][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:07.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.638][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.640][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:07.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:07.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:07.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:07.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:07.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:07.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:07.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:07.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:07.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:07.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:07.705][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-02 05:24:07.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:07.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:07.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:07.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:07.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:07.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:07.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:07.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:07.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:07.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:07.755][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-02 05:24:07.757][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:07.759][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-02 05:24:07.761][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:07.763][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:07.765][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:07.766][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:07.768][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:07.769][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:07.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:07.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:07.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:07.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:07.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:07.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:07.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:07.789][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-11-02 05:24:07.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:07.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:07.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-11-02 05:24:08.551][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-11-02 05:24:09.281][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:09.284][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-11-02 05:24:09.289][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-11-02 05:24:09.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-11-02 05:24:09.294][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:09.296][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:09.297][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:09.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:09.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:09.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:09.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:09.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:09.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:09.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:09.315][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.317][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.328][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.335][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:09.337][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:09.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.339][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.341][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:09.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:09.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.347][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:09.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:09.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.351][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:09.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:09.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.358][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:09.359][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:09.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.362][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:09.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:09.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.369][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:09.371][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:09.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.373][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:09.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:09.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.381][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:09.382][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:09.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.385][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.387][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:09.388][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.391][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:09.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.398][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:09.400][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:09.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.402][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:09.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.409][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:09.411][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:09.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.413][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:09.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:09.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.421][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:09.423][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:09.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.425][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.427][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:09.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:09.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.433][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:09.434][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:09.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.437][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.438][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:09.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:09.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:09.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:09.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:09.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:09.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:09.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:09.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:09.515][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-02 05:24:09.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:09.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:09.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:09.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:09.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:09.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:09.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:09.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:09.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:09.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:09.548][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-02 05:24:09.549][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:09.551][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-02 05:24:09.553][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:09.554][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:09.556][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:09.557][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:09.559][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:09.560][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:09.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:09.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:09.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:09.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:09.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:09.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:09.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:09.579][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-11-02 05:24:09.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:09.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:09.586][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-11-02 05:24:10.313][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-11-02 05:24:11.039][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:11.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-11-02 05:24:11.047][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-11-02 05:24:11.051][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-11-02 05:24:11.053][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:11.054][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:11.056][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:11.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:11.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:11.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:11.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:11.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:11.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:11.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:11.075][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.077][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.079][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.087][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:11.088][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:11.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.091][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.093][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:11.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:11.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.098][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:11.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:11.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.103][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:11.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:11.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.111][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:11.112][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:11.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.115][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:11.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:11.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.123][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:11.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:11.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.128][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:11.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:11.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.135][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:11.137][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:11.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.140][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.142][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:11.144][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.146][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.148][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:11.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:11.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:11.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.159][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:11.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:11.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.167][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:11.168][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:11.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.171][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:11.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:11.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.180][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:11.182][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:11.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.185][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.186][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:11.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:11.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.206][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:11.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:11.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.211][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:11.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:11.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:11.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:11.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:11.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:11.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:11.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:11.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:11.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:11.273][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-02 05:24:11.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:11.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:11.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:11.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:11.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:11.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:11.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:11.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:11.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:11.305][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-02 05:24:11.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:11.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-02 05:24:11.311][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:11.312][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:11.314][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:11.315][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:11.316][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:11.318][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:11.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:11.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:11.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:11.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:11.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:11.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:11.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:11.336][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-11-02 05:24:11.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:11.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:11.343][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-11-02 05:24:12.073][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-11-02 05:24:12.798][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:12.801][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-11-02 05:24:12.807][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-11-02 05:24:12.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-11-02 05:24:12.813][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:12.815][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:12.817][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:12.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:12.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:12.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:12.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:12.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:12.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:12.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:12.836][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:12.838][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:12.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.841][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.850][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:12.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:12.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.855][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:12.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:12.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.864][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:12.866][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:12.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.869][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.871][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:12.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.878][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:12.880][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:12.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.883][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:12.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:12.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.892][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:12.894][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:12.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.897][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:12.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.906][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:12.908][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:12.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.910][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.912][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:12.928][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:12.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.931][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.932][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:12.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.938][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:12.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:12.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.942][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:12.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:12.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.949][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:12.951][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:12.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.953][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:12.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:12.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.961][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:12.962][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:12.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.965][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.967][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:12.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:12.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.972][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:12.974][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:12.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.976][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:12.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:12.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:12.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:12.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:12.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:12.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:12.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:12.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:12.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:13.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:13.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:13.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:13.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:13.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:13.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:13.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:13.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:13.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:13.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:13.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:13.038][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-02 05:24:13.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:13.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:13.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:13.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:13.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:13.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:13.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:13.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:13.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:13.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:13.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:13.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:13.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:13.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:13.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:13.070][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-02 05:24:13.071][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:13.074][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-02 05:24:13.075][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:13.077][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:13.078][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:13.080][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:13.081][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:13.083][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:13.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:13.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:13.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:13.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:13.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:13.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:13.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:13.102][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-11-02 05:24:13.106][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:13.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:13.110][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-11-02 05:24:13.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-11-02 05:24:14.565][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:14.572][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-11-02 05:24:14.580][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-11-02 05:24:14.585][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-11-02 05:24:14.588][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:14.591][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:14.594][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:14.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:14.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:14.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:14.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:14.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:14.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:14.617][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[2024-11-02 05:24:14.625][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.631][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.641][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:14.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:14.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.647][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:14.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:14.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.744][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:14.746][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:14.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.750][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:14.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:14.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.761][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:14.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:14.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.767][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:14.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:14.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:14.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:14.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.784][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:14.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:14.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.792][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:14.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:14.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.799][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:14.800][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.803][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.805][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:14.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.811][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:14.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:14.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.815][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:14.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:14.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.827][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:14.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.835][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:14.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:14.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.839][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.841][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.847][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:14.848][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:14.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.851][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:14.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:14.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:14.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:14.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:14.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:14.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:14.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:14.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:14.932][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-02 05:24:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:14.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:14.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:14.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:14.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:14.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:14.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:14.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:14.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:14.972][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-02 05:24:14.974][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:14.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-02 05:24:14.977][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:14.979][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:14.980][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:14.982][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:14.983][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:14.984][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:14.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:14.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:14.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:14.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:14.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:15.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:15.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:15.002][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-11-02 05:24:15.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:15.008][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:15.010][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-11-02 05:24:15.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-11-02 05:24:16.459][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:16.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-11-02 05:24:16.481][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-11-02 05:24:16.484][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-11-02 05:24:16.486][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:16.488][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:16.490][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:16.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:16.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:16.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:16.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:16.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:16.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:16.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:16.508][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.510][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.520][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:16.521][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:16.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.526][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:16.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:16.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.531][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:16.533][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:16.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.535][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:16.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:16.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.543][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:16.544][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:16.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.547][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:16.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:16.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:16.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.559][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:16.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:16.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.566][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:16.567][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:16.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.570][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.572][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:16.573][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.576][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:16.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:16.584][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:16.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.587][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:16.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.594][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:16.595][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:16.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.598][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:16.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.605][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:16.606][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:16.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.609][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.611][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:16.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:16.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.616][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:16.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:16.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.620][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.622][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:16.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:16.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:16.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:16.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:16.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:16.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:16.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:16.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:16.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:16.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:16.684][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-02 05:24:16.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:16.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:16.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:16.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:16.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:16.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:16.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:16.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:16.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:16.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:16.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:16.716][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-02 05:24:16.727][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:16.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-02 05:24:16.732][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:16.733][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:16.735][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:16.736][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:16.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:16.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:16.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:16.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:16.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:16.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:16.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:16.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:16.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:16.759][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-11-02 05:24:16.763][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:16.764][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:16.766][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-11-02 05:24:17.491][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-11-02 05:24:18.205][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:18.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-11-02 05:24:18.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-11-02 05:24:18.217][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-11-02 05:24:18.219][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:18.221][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:18.223][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:18.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:18.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:18.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:18.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:18.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:18.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:18.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:18.244][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.249][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.257][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:18.259][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:18.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.262][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.264][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:18.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:18.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.271][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:18.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:18.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.275][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.278][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:18.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:18.286][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:18.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.289][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:18.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.297][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:18.299][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:18.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.302][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:18.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:18.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.310][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:18.312][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:18.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.315][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.317][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:18.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:18.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.329][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:18.331][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:18.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:18.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:18.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.342][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:18.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:18.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.347][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:18.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:18.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.356][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:18.357][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:18.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.360][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.362][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:18.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:18.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.368][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:18.370][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:18.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.373][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:18.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:18.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:18.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:18.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:18.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:18.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:18.459][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-02 05:24:18.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:18.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:18.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:18.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:18.509][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:24:18.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:18.516][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:18.520][private$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[2024-11-02 05:24:19.441][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[2024-11-02 05:24:20.303][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:20.306][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-02 05:24:20.311][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-02 05:24:20.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.445][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.TRACE[2024-11-02 05:24:20.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.565][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.TRACE[2024-11-02 05:24:20.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:20.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:20.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:20.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:20.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:20.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:20.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:20.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:20.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:20.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:20.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:20.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:21.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:21.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:21.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:21.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:21.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:21.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:21.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:21.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:21.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:21.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:24:21.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:21.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:21.101][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:21.807][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:22.562][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:22.565][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-11-02 05:24:22.570][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-11-02 05:24:22.575][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:24:22.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:22.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:22.584][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:23.312][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:24.036][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:24.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-11-02 05:24:24.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-11-02 05:24:24.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:24.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:24.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:24.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:24.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:24.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:24.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:24.064][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-02 05:24:24.065][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:24.068][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-02 05:24:24.069][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:24.071][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:24.072][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:24.074][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:24.075][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:24.076][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:24.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:24.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:24.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:24.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:24.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:24.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:24.094][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[2024-11-02 05:24:24.095][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-11-02 05:24:24.100][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:24.101][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:24.103][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-11-02 05:24:24.828][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-11-02 05:24:26.624][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:26.627][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-11-02 05:24:26.632][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-11-02 05:24:26.636][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-11-02 05:24:26.638][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:26.640][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:26.642][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:26.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:26.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:26.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:26.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:26.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:26.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:26.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:26.686][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.688][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.691][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.699][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:26.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:26.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.703][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.705][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:26.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:26.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.711][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:26.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:26.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.715][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:26.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:26.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.723][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:26.725][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:26.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.727][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:26.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:26.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.735][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:26.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:26.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.740][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:26.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:26.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.748][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:26.749][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:26.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.752][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.754][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:26.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:26.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.761][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:26.762][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:26.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.767][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:26.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:26.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.773][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.777][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.785][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:26.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:26.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.789][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.797][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:26.799][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:26.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.801][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.803][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:26.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:26.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.809][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:26.810][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:26.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.813][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.815][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:26.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:26.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:26.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:26.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:26.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:26.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:26.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:26.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:26.880][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-02 05:24:26.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:26.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:26.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:26.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:26.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:26.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:26.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:26.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:26.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:26.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:26.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:26.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:26.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:26.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:26.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:26.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:26.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:26.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:26.953][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-02 05:24:26.955][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:26.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-02 05:24:26.959][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:26.961][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:26.962][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:26.964][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:26.965][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:26.966][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:26.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:26.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:26.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:26.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:26.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:26.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:26.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:26.985][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-11-02 05:24:26.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:26.991][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:26.993][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-11-02 05:24:27.697][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-11-02 05:24:29.149][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:29.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-11-02 05:24:29.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-11-02 05:24:29.160][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-11-02 05:24:29.163][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:29.164][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:29.166][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:29.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.185][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.186][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.189][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.196][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:29.198][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:29.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.200][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.202][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:29.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:29.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.207][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:29.209][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:29.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.211][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:29.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:29.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.218][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:29.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:29.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.222][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:29.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:29.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:29.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:29.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.233][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.240][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:29.241][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:29.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.244][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.246][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:29.247][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:29.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:29.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:29.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.257][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.258][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.261][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.268][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:29.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:29.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.272][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.280][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:29.281][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:29.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.284][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.292][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:29.293][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:29.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.296][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:29.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:29.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:29.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:29.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:29.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:29.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.375][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-02 05:24:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.417][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[2024-11-02 05:24:29.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:29.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-02 05:24:29.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:29.428][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-02 05:24:29.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.445][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.TRACE[2024-11-02 05:24:29.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.557][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.TRACE[2024-11-02 05:24:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.608][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.TRACE[2024-11-02 05:24:29.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.899][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.TRACE[2024-11-02 05:24:29.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:29.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:29.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:29.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:29.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:29.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:29.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:29.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:29.989][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[2024-11-02 05:24:29.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:29.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:29.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:29.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.092][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[2024-11-02 05:24:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.136][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[2024-11-02 05:24:30.140][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:30.143][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-02 05:24:30.144][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:30.146][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-02 05:24:30.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.239][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.TRACE[2024-11-02 05:24:30.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.335][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.TRACE[2024-11-02 05:24:30.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:30.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:30.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.868][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:30.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:30.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 05:24:30.884][biodb::testThat]
biodb.INFO [2024-11-02 05:24:30.886][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-02 05:24:30.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:30.889][biodb::testThat]
biodb.TRACE[2024-11-02 05:24:30.894][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 05:24:30.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 05:24:30.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:30.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:30.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:30.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:30.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:30.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:30.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:30.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:30.948][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[2024-11-02 05:24:30.952][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:30.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:30.957][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:31.685][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:32.411][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:32.414][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-02 05:24:32.419][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-02 05:24:32.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:32.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:32.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:32.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:32.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:32.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:32.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:32.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:32.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:32.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:32.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:32.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:32.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:32.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:32.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:32.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:32.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:32.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:32.453][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:24:32.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:32.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:32.462][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:33.903][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:34.638][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:34.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-02 05:24:34.646][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-02 05:24:34.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:34.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:34.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:34.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:34.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:34.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:34.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:34.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:34.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:34.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:34.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:34.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:34.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:34.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:34.692][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[2024-11-02 05:24:34.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:34.709][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-02 05:24:34.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:34.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:34.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:34.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:34.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:34.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:34.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:34.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.757][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.758][private$selectFields]
biodb.TRACE[2024-11-02 05:24:34.760][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:34.761][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:34.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.765][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.767][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.769][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.770][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.775][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.781][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.782][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:34.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.814][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-02 05:24:34.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:34.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:34.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:34.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:34.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:34.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:34.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.842][private$selectFields]
biodb.TRACE[2024-11-02 05:24:34.843][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:34.844][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:34.846][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.847][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.848][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.851][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.857][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.858][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.860][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.861][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.867][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.885][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-02 05:24:34.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:34.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:34.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:34.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:34.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:34.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:34.899][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.TRACE[2024-11-02 05:24:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.912][private$selectFields]
biodb.TRACE[2024-11-02 05:24:34.913][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:34.914][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:34.916][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.917][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.918][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.921][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.923][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.926][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.927][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.928][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:34.930][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.934][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.935][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:34.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:34.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.952][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-02 05:24:34.953][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-02 05:24:34.955][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-02 05:24:34.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:35.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:35.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:35.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:35.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:35.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:35.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:35.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:35.094][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[2024-11-02 05:24:35.099][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:35.100][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:35.103][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:35.832][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:36.558][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:36.561][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-11-02 05:24:36.566][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-11-02 05:24:36.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:24:36.575][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:36.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:36.579][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:37.847][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:40.110][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:40.113][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-11-02 05:24:40.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-11-02 05:24:40.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.187][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.TRACE[2024-11-02 05:24:40.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:40.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.274][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-02 05:24:40.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.337][private$selectFields]
biodb.TRACE[2024-11-02 05:24:40.338][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:40.340][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:40.341][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.342][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.347][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.349][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.350][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.353][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.356][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.362][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.363][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:40.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.383][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-02 05:24:40.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.470][private$selectFields]
biodb.TRACE[2024-11-02 05:24:40.472][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:40.473][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:40.475][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.480][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.482][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.483][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.486][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.503][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.505][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.506][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.509][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.511][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:40.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.532][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-02 05:24:40.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.548][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.TRACE[2024-11-02 05:24:40.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.561][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.563][private$selectFields]
biodb.TRACE[2024-11-02 05:24:40.564][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:40.565][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:40.566][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.568][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.569][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.572][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.573][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.578][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.579][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.580][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.586][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.587][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:40.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.605][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-02 05:24:40.607][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-02 05:24:40.608][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-02 05:24:40.620][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:40.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:40.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 05:24:40.630][biodb::testThat]
biodb.INFO [2024-11-02 05:24:40.632][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-02 05:24:40.633][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:40.634][biodb::testThat]
biodb.TRACE[2024-11-02 05:24:40.639][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 05:24:40.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 05:24:40.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.700][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[2024-11-02 05:24:40.705][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[2024-11-02 05:24:40.710][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:40.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-02 05:24:40.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:40.717][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-02 05:24:40.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.762][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[2024-11-02 05:24:40.767][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:40.769][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-02 05:24:40.771][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:40.773][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-02 05:24:40.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:40.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:40.845][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-02 05:24:40.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.875][private$selectFields]
biodb.TRACE[2024-11-02 05:24:40.876][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:40.877][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:40.879][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.882][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.885][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.886][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.888][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.893][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.894][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.897][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.900][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.901][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:40.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.922][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-02 05:24:40.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:40.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:40.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:40.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:40.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:40.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:40.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:40.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.961][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.963][private$selectFields]
biodb.TRACE[2024-11-02 05:24:40.965][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:40.966][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:40.967][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.969][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.971][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.973][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.975][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.976][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.979][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.981][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.982][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:40.984][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.988][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.989][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:40.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:40.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:40.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:40.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.009][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-02 05:24:41.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.037][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.039][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.040][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.041][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.044][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.048][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.051][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.054][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.057][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.058][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.059][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.062][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.063][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.084][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-02 05:24:41.086][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-02 05:24:41.087][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-02 05:24:41.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:41.141][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[2024-11-02 05:24:41.146][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:41.148][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-02 05:24:41.149][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:41.151][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-02 05:24:41.156][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[2024-11-02 05:24:41.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:41.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-02 05:24:41.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:41.166][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-02 05:24:41.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.182][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.TRACE[2024-11-02 05:24:41.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.223][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.TRACE[2024-11-02 05:24:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.277][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-02 05:24:41.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.307][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.309][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.310][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.312][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.313][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.314][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.316][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.320][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.321][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.324][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.325][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.327][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.328][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.330][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.334][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.353][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-02 05:24:41.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.381][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.383][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.384][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.391][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.393][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.394][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.397][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.400][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.405][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.407][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.426][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-02 05:24:41.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.466][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.468][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.469][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.471][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.477][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.478][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.482][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.485][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.487][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.493][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.512][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-02 05:24:41.514][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-02 05:24:41.515][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-02 05:24:41.528][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:41.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:41.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 05:24:41.540][biodb::testThat]
biodb.INFO [2024-11-02 05:24:41.541][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-02 05:24:41.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:41.544][biodb::testThat]
biodb.TRACE[2024-11-02 05:24:41.549][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 05:24:41.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 05:24:41.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:41.603][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[2024-11-02 05:24:41.608][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:41.610][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-02 05:24:41.612][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:41.614][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-02 05:24:41.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.651][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[2024-11-02 05:24:41.656][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:41.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-02 05:24:41.660][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:41.662][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-02 05:24:41.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.679][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.TRACE[2024-11-02 05:24:41.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.720][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.TRACE[2024-11-02 05:24:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:41.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:41.739][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-02 05:24:41.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.771][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.773][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.774][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.776][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.781][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.783][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.787][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.789][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.790][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.792][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.793][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.798][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.819][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-02 05:24:41.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.851][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.852][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.854][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.855][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.857][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.866][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.872][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.874][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.880][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.881][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.899][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-02 05:24:41.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:41.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:41.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:41.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:41.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:41.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:41.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:41.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.926][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.928][private$selectFields]
biodb.TRACE[2024-11-02 05:24:41.929][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:41.930][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:41.932][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.937][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.940][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.942][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.944][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.945][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:41.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.948][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.950][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.951][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:41.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:41.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:41.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:41.980][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-02 05:24:41.981][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-02 05:24:41.982][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-02 05:24:42.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:42.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:42.061][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[2024-11-02 05:24:42.066][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:42.068][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-02 05:24:42.070][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:42.072][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-02 05:24:42.077][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[2024-11-02 05:24:42.082][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:42.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-02 05:24:42.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:42.088][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-02 05:24:42.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:42.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:42.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:42.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:42.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:42.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:42.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:42.187][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-02 05:24:42.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.201][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.TRACE[2024-11-02 05:24:42.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.215][private$selectFields]
biodb.TRACE[2024-11-02 05:24:42.217][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:42.218][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:42.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.232][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.235][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.242][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.243][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.245][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.251][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.252][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:42.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.271][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-02 05:24:42.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:42.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.299][private$selectFields]
biodb.TRACE[2024-11-02 05:24:42.301][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:42.302][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:42.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.309][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.310][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.312][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.314][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.316][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.317][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.323][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.324][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:42.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.342][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-02 05:24:42.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:42.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.370][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.372][private$selectFields]
biodb.TRACE[2024-11-02 05:24:42.373][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-02 05:24:42.374][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-02 05:24:42.376][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.379][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.382][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.384][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.385][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.388][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.390][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.391][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-02 05:24:42.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.394][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.397][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.399][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-02 05:24:42.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:42.419][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-02 05:24:42.421][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-02 05:24:42.422][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-02 05:24:42.448][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:42.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-02 05:24:42.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:42.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 05:24:42.458][biodb::testThat]
biodb.INFO [2024-11-02 05:24:42.460][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-02 05:24:42.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:42.462][biodb::testThat]
biodb.DEBUG[2024-11-02 05:24:42.465][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-02 05:24:42.466][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:24:42.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-02 05:24:42.470][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:24:42.480][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:42.482][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:42.484][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:42.486][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:42.487][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:42.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:42.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:42.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:42.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:42.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:42.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:42.504][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[2024-11-02 05:24:42.506][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-11-02 05:24:42.510][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:42.512][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:42.514][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-11-02 05:24:44.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-11-02 05:24:45.450][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:45.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-11-02 05:24:45.458][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-11-02 05:24:45.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-11-02 05:24:45.464][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:45.466][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:24:45.467][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:45.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:45.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:45.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:45.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:45.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:45.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:45.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:45.486][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.487][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.490][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.497][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:45.499][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:45.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.501][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.503][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:45.505][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:45.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.507][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.509][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:45.511][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:45.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.515][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:45.516][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:45.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.519][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.520][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:45.522][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:45.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.526][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:45.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:45.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.530][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.531][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:45.533][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:45.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.535][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.537][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:45.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:45.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.540][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.542][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:45.544][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:45.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.546][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.548][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:45.549][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:45.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.551][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:45.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:45.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:45.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:45.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:45.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:45.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:45.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:45.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:45.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:45.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:45.604][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-02 05:24:45.606][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-02 05:24:45.616][biodb::testThat]
biodb.INFO [2024-11-02 05:24:45.617][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-02 05:24:45.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:45.619][biodb::testThat]
biodb.DEBUG[2024-11-02 05:24:45.633][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-02 05:24:45.635][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-02 05:24:45.636][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-02 05:24:45.638][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-02 05:24:45.640][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-11-02 05:24:45.641][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:24:45.652][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:24:45.658][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:45.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:24:45.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:24:45.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:45.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:45.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:45.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:45.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:45.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:45.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:45.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-11-02 05:24:45.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:45.686][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:45.688][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-11-02 05:24:46.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-11-02 05:24:47.144][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:47.147][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-11-02 05:24:47.151][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-11-02 05:24:47.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:47.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:47.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:47.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:47.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:47.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:47.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:47.168][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-11-02 05:24:47.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:47.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:47.176][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-11-02 05:24:47.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-11-02 05:24:48.659][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:48.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-11-02 05:24:48.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-11-02 05:24:48.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:48.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:48.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:48.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:48.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:48.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:48.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:48.682][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-11-02 05:24:48.686][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:48.687][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:48.689][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-11-02 05:24:49.415][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-11-02 05:24:50.141][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:50.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-11-02 05:24:50.149][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-11-02 05:24:50.152][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-11-02 05:24:50.154][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:24:50.156][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-02 05:24:50.157][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-02 05:24:50.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:50.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:50.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:50.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:50.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:50.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:50.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:24:50.212][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.214][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.217][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.226][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:50.227][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:50.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.230][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.232][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:50.234][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:50.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.239][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:50.241][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:50.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.244][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.247][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.252][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.254][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.257][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.259][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:50.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:50.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.264][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.266][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.267][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.270][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.273][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:50.274][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:50.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.277][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.279][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:50.281][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:50.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.284][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.286][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:50.287][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:50.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.290][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:50.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:50.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:50.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:50.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:50.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:50.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:50.408][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.TRACE[2024-11-02 05:24:50.411][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.413][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.416][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.425][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:50.427][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:50.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.431][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.433][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:50.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.440][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:50.442][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:50.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.445][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:50.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.455][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:50.457][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:50.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.461][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:50.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:50.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.470][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.472][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.475][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.484][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.486][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.490][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.492][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.499][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:50.501][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:50.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.504][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.506][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:50.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:50.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.513][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.514][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.517][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.524][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:50.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:50.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.528][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:50.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:50.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.535][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:50.537][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:50.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.539][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.541][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:50.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:50.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.546][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:50.548][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:50.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.550][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:50.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:50.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:50.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:50.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:50.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:50.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:50.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:50.607][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.TRACE[2024-11-02 05:24:50.610][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.614][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.621][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:50.623][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:50.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.625][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.627][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:24:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:24:50.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.642][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:50.644][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:50.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.646][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:24:50.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:24:50.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.654][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:50.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:50.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.657][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:24:50.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:24:50.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.665][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.666][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.669][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:24:50.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.676][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.677][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.680][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:24:50.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.687][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:50.688][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:50.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.691][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.693][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:24:50.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:24:50.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.698][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.702][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.709][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:50.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:50.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.713][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:50.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.720][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:50.722][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:50.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.724][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.726][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:24:50.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:24:50.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.732][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:50.733][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:50.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.736][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:24:50.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:24:50.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:24:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:50.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:24:50.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:24:50.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:50.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:24:50.828][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-02 05:24:50.829][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-02 05:24:50.831][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-02 05:24:50.847][biodb::testThat]
biodb.INFO [2024-11-02 05:24:50.849][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-02 05:24:50.850][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:50.851][biodb::testThat]
biodb.INFO [2024-11-02 05:24:50.894][biodb::testThat]
biodb.INFO [2024-11-02 05:24:50.895][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-02 05:24:50.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:50.898][biodb::testThat]
biodb.INFO [2024-11-02 05:24:50.908][biodb::testThat]
biodb.INFO [2024-11-02 05:24:50.909][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-02 05:24:50.910][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:50.912][biodb::testThat]
biodb.DEBUG[2024-11-02 05:24:50.915][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[2024-11-02 05:24:50.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:50.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:50.924][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:51.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:52.718][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:52.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-11-02 05:24:52.726][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-11-02 05:24:52.741][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:24:52.743][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:24:52.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:52.745][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:24:52.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:52.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:24:52.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:24:52.750][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 05:24:52.752][biodb::testThat]
biodb.INFO [2024-11-02 05:24:52.753][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-02 05:24:52.755][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:52.756][biodb::testThat]
biodb.ERROR[2024-11-02 05:24:52.775][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-02 05:24:52.800][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-02 05:24:52.818][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 05:24:52.820][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-02 05:24:52.821][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-02 05:24:52.823][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 05:24:52.824][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:52.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:52.826][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:52.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:52.829][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-02 05:24:52.845][biodb::testContext]
biodb.INFO [2024-11-02 05:24:52.847][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:24:52.848][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-02 05:24:52.849][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:24:52.851][biodb::testContext]
biodb.INFO [2024-11-02 05:24:52.853][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:24:52.856][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 05:24:52.860][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:24:52.862][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 05:24:52.863][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 05:24:52.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.868][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 05:24:52.870][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 05:24:52.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.874][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 05:24:52.876][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 05:24:52.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.881][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 05:24:52.882][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 05:24:52.883][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 05:24:52.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.903][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 05:24:52.904][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 05:24:52.906][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 05:24:52.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.911][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 05:24:52.912][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 05:24:52.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.917][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 05:24:52.918][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 05:24:52.920][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 05:24:52.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.923][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[2024-11-02 05:24:52.925][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 05:24:52.926][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 05:24:52.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.931][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 05:24:52.932][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 05:24:52.934][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 05:24:52.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.939][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:24:52.940][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 05:24:52.941][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 05:24:52.943][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 05:24:52.944][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 05:24:52.945][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 05:24:52.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.950][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 05:24:52.952][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 05:24:52.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.957][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 05:24:52.958][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 05:24:52.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.963][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 05:24:52.964][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 05:24:52.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.969][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 05:24:52.970][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 05:24:52.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.975][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 05:24:52.977][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 05:24:52.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.980][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[2024-11-02 05:24:52.982][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:24:52.983][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 05:24:52.988][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 05:24:52.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:52.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:52.993][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 05:24:52.994][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 05:24:52.996][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 05:24:52.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:52.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.001][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 05:24:53.004][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.005][self$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[2024-11-02 05:24:53.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.008][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:24:53.010][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.011][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.012][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.014][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.015][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:24:53.017][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:24:53.018][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.020][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 05:24:53.021][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:24:53.022][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.024][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.025][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:24:53.025][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:24:53.025][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:24:53.025][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:24:53.025][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:24:53.027][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:24:53.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:24:53.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.036][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:24:53.039][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:24:53.040][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.041][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.043][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 05:24:53.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.047][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:24:53.048][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.050][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:24:53.051][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.052][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.054][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.056][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:24:53.058][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:24:53.059][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.061][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 05:24:53.062][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:24:53.063][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.065][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.066][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:24:53.066][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:24:53.066][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:24:53.066][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:24:53.066][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:24:53.068][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:24:53.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:24:53.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.077][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:24:53.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:24:53.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.082][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.084][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 05:24:53.086][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.088][self$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[2024-11-02 05:24:53.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:24:53.092][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.096][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.097][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:24:53.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:24:53.100][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.101][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 05:24:53.103][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:24:53.104][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.105][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.107][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:24:53.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.112][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:24:53.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.117][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.118][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:24:53.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:24:53.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.391][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.393][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 05:24:53.395][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.397][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:24:53.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.399][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:24:53.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.406][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:24:53.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:24:53.409][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.410][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 05:24:53.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:24:53.413][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.415][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.417][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:24:53.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.420][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:24:53.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.424][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.426][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.427][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:24:53.428][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:24:53.429][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.431][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:24:53.432][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:24:53.434][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.435][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[2024-11-02 05:24:53.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.441][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[2024-11-02 05:24:53.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.453][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[2024-11-02 05:24:53.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.538][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[2024-11-02 05:24:53.539][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 05:24:53.541][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 05:24:53.543][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 05:24:53.545][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 05:24:53.547][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:24:53.549][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 05:24:53.551][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 05:24:53.553][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 05:24:53.555][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 05:24:53.557][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 05:24:53.558][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:24:53.560][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 05:24:53.562][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 05:24:53.564][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 05:24:53.566][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 05:24:53.568][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 05:24:53.570][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 05:24:53.572][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 05:24:53.574][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:24:53.576][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 05:24:53.578][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 05:24:53.580][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 05:24:53.582][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 05:24:53.584][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 05:24:53.586][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 05:24:53.588][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 05:24:53.589][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 05:24:53.591][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 05:24:53.593][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 05:24:53.595][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 05:24:53.597][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 05:24:53.599][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 05:24:53.601][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 05:24:53.602][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 05:24:53.604][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 05:24:53.606][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 05:24:53.608][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 05:24:53.610][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 05:24:53.612][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 05:24:53.614][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 05:24:53.622][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 05:24:53.624][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 05:24:53.626][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 05:24:53.628][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 05:24:53.630][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 05:24:53.632][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 05:24:53.634][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 05:24:53.636][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 05:24:53.638][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 05:24:53.640][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 05:24:53.642][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 05:24:53.644][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 05:24:53.646][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 05:24:53.648][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 05:24:53.649][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 05:24:53.651][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 05:24:53.653][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 05:24:53.655][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 05:24:53.657][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 05:24:53.659][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 05:24:53.661][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 05:24:53.663][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 05:24:53.665][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 05:24:53.667][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 05:24:53.669][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 05:24:53.671][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 05:24:53.673][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:24:53.675][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:24:53.677][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 05:24:53.679][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 05:24:53.681][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 05:24:53.683][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 05:24:53.685][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 05:24:53.687][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 05:24:53.689][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 05:24:53.691][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 05:24:53.693][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 05:24:53.695][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 05:24:53.697][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 05:24:53.699][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 05:24:53.701][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 05:24:53.703][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 05:24:53.705][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 05:24:53.707][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 05:24:53.709][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:24:53.710][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:24:53.711][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.714][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.715][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[2024-11-02 05:24:53.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.724][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[2024-11-02 05:24:53.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.732][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[2024-11-02 05:24:53.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.741][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[2024-11-02 05:24:53.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.749][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.DEBUG[2024-11-02 05:24:53.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.767][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[2024-11-02 05:24:53.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.846][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[2024-11-02 05:24:53.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.862][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[2024-11-02 05:24:53.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:24:53.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:53.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:53.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:53.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:53.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:53.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:53.874][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-02 05:24:53.877][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-02 05:24:53.879][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.881][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.882][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:24:53.885][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.886][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.888][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.889][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-02 05:24:53.890][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 05:24:53.892][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:24:53.893][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.894][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-02 05:24:53.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-02 05:24:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-02 05:24:53.899][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 05:24:53.900][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:24:53.900][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:24:53.900][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:24:53.902][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 05:24:53.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:24:53.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:24:53.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:24:53.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:24:53.911][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:24:53.911][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-02 05:24:53.912][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:24:53.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:24:53.915][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 05:24:53.916][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-02 05:24:53.916][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-02 05:24:53.918][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:24:53.920][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:24:53.922][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-02 05:24:53.924][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:24:53.927][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:24:53.929][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:24:53.934][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-02 05:24:53.936][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-02 05:24:53.937][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-02 05:24:53.940][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-02 05:24:53.941][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:24:53.943][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:24:53.945][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-02 05:24:53.946][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-02 05:24:53.948][biodb::testThat]
biodb.INFO [2024-11-02 05:24:53.949][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-02 05:24:53.951][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:24:53.952][biodb::testThat]
biodb.DEBUG[2024-11-02 05:24:53.957][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-02 05:24:53.962][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:53.963][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:53.965][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-11-02 05:24:54.685][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-11-02 05:24:55.586][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:55.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-11-02 05:24:55.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-11-02 05:24:55.598][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[2024-11-02 05:24:55.602][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:55.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:55.606][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:56.309][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:24:57.034][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:57.037][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-11-02 05:24:57.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-11-02 05:24:57.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:57.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:57.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:57.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:57.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:57.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:57.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:57.060][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:24:57.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:57.066][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:57.068][private$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[2024-11-02 05:24:57.826][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[2024-11-02 05:24:58.551][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:24:58.554][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-11-02 05:24:58.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-11-02 05:24:58.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.574][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[2024-11-02 05:24:58.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:58.637][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[2024-11-02 05:24:58.642][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:58.644][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-02 05:24:58.645][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:58.647][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-02 05:24:58.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:58.664][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[2024-11-02 05:24:58.669][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:58.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-02 05:24:58.672][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:58.674][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-02 05:24:58.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.689][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.DEBUG[2024-11-02 05:24:58.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:58.708][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[2024-11-02 05:24:58.712][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:58.714][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-02 05:24:58.716][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:58.718][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-02 05:24:58.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.732][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[2024-11-02 05:24:58.735][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[2024-11-02 05:24:58.739][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:24:58.742][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-02 05:24:58.744][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:24:58.746][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-02 05:24:58.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:24:58.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:24:58.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:24:58.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:24:58.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:24:58.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:24:58.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:24:58.764][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[2024-11-02 05:24:58.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:24:58.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:24:58.773][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:24:59.499][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:25:00.224][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:25:00.226][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-11-02 05:25:00.231][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-11-02 05:25:00.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:25:00.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:00.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:00.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:00.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:00.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:00.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-02 05:25:00.254][biodb::testThat]
biodb.INFO [2024-11-02 05:25:00.255][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-02 05:25:00.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:25:00.258][biodb::testThat]
biodb.DEBUG[2024-11-02 05:25:00.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:25:00.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:25:00.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:25:00.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:25:00.975][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:25:01.730][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:25:01.733][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-11-02 05:25:01.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-11-02 05:25:01.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:25:01.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:01.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:01.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:01.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:01.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:01.754][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[2024-11-02 05:25:01.760][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[2024-11-02 05:25:01.764][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:25:01.765][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:25:01.768][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-02 05:25:02.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-02 05:25:03.226][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:25:03.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-11-02 05:25:03.253][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-11-02 05:25:03.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:25:03.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-02 05:25:03.274][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 05:25:03.276][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-02 05:25:03.277][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-02 05:25:03.279][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 05:25:03.280][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.282][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.285][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-02 05:25:03.291][biodb::testContext]
biodb.INFO [2024-11-02 05:25:03.293][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:25:03.294][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-02 05:25:03.295][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:25:03.297][biodb::testContext]
biodb.INFO [2024-11-02 05:25:03.299][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:25:03.301][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 05:25:03.306][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:25:03.307][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 05:25:03.309][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 05:25:03.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.314][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 05:25:03.315][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 05:25:03.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.320][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 05:25:03.321][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 05:25:03.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.326][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 05:25:03.327][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 05:25:03.329][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 05:25:03.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.334][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 05:25:03.335][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 05:25:03.337][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 05:25:03.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.342][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 05:25:03.343][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 05:25:03.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.348][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 05:25:03.350][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 05:25:03.351][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 05:25:03.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.356][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 05:25:03.357][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 05:25:03.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.362][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 05:25:03.363][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 05:25:03.365][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 05:25:03.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.370][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:25:03.371][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 05:25:03.372][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 05:25:03.374][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 05:25:03.375][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 05:25:03.376][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 05:25:03.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.381][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 05:25:03.382][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 05:25:03.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.387][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 05:25:03.389][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 05:25:03.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.393][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 05:25:03.395][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 05:25:03.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.400][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 05:25:03.401][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 05:25:03.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.406][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 05:25:03.407][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 05:25:03.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.412][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:25:03.413][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 05:25:03.418][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 05:25:03.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.424][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 05:25:03.425][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 05:25:03.427][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 05:25:03.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.432][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 05:25:03.435][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.436][self$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[2024-11-02 05:25:03.438][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.439][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:03.441][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.442][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.444][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.445][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.447][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:25:03.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:03.450][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.451][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 05:25:03.453][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:03.454][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.456][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.457][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:25:03.457][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:25:03.457][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:25:03.457][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:25:03.457][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:25:03.459][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:03.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.463][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:03.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.467][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.469][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.470][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:03.471][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:03.473][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.474][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.476][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 05:25:03.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.480][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:25:03.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:03.484][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.485][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.496][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.498][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:25:03.499][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:03.500][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.502][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 05:25:03.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:03.505][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.506][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.507][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:25:03.507][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:25:03.507][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:25:03.507][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:25:03.507][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:25:03.509][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:03.510][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.513][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:03.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.518][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:03.521][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:03.522][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.524][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.526][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 05:25:03.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.529][self$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[2024-11-02 05:25:03.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:03.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.536][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.539][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:25:03.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:03.542][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.543][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 05:25:03.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:03.546][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.547][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.548][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.550][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:03.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.554][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:03.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.557][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.559][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.560][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:03.561][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:03.563][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.564][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.566][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 05:25:03.568][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.569][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:25:03.571][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.572][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:03.573][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.575][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.576][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.578][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.579][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:25:03.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:03.582][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.583][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 05:25:03.584][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:03.586][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.587][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:03.588][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.590][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:03.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:03.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:03.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:03.598][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:03.599][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:03.602][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:03.603][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:03.604][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:03.606][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:25:03.608][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.635][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[2024-11-02 05:25:03.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.661][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[2024-11-02 05:25:03.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.693][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[2024-11-02 05:25:03.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.718][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[2024-11-02 05:25:03.720][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 05:25:03.721][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 05:25:03.723][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 05:25:03.732][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 05:25:03.734][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:25:03.736][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 05:25:03.738][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 05:25:03.740][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 05:25:03.742][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 05:25:03.744][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 05:25:03.746][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:25:03.748][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 05:25:03.750][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 05:25:03.752][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 05:25:03.754][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 05:25:03.756][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 05:25:03.758][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 05:25:03.760][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 05:25:03.762][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:25:03.764][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 05:25:03.766][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 05:25:03.768][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 05:25:03.770][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 05:25:03.772][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 05:25:03.774][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 05:25:03.776][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 05:25:03.778][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 05:25:03.780][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 05:25:03.782][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 05:25:03.784][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 05:25:03.785][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 05:25:03.787][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 05:25:03.789][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 05:25:03.791][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 05:25:03.793][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 05:25:03.795][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 05:25:03.797][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 05:25:03.798][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 05:25:03.800][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 05:25:03.802][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 05:25:03.804][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 05:25:03.806][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 05:25:03.808][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 05:25:03.810][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 05:25:03.812][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 05:25:03.814][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 05:25:03.815][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 05:25:03.817][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 05:25:03.819][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 05:25:03.821][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 05:25:03.823][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 05:25:03.825][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 05:25:03.827][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 05:25:03.829][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 05:25:03.830][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 05:25:03.832][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 05:25:03.834][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 05:25:03.836][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 05:25:03.838][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 05:25:03.840][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 05:25:03.842][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 05:25:03.843][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 05:25:03.845][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 05:25:03.847][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 05:25:03.849][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 05:25:03.851][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 05:25:03.853][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:25:03.855][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:25:03.857][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 05:25:03.858][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 05:25:03.860][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 05:25:03.862][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 05:25:03.864][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 05:25:03.866][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 05:25:03.868][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 05:25:03.870][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 05:25:03.872][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 05:25:03.873][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 05:25:03.875][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 05:25:03.877][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 05:25:03.879][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 05:25:03.881][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 05:25:03.883][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 05:25:03.885][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 05:25:03.887][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:25:03.888][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:25:03.889][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.892][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.934][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[2024-11-02 05:25:03.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.942][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[2024-11-02 05:25:03.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.975][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[2024-11-02 05:25:03.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:03.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.991][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[2024-11-02 05:25:03.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:03.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:03.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:03.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:03.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:03.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:03.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:04.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:04.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:04.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:04.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:04.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:04.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:04.008][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[2024-11-02 05:25:04.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:04.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:04.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:04.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:04.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:04.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:04.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:04.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:04.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:04.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:04.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:04.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:04.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:04.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:04.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:04.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:04.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:04.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:04.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:04.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:04.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:04.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:04.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:04.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:04.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:04.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:04.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:04.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:04.043][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-02 05:25:04.045][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-02 05:25:04.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:04.049][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 05:25:04.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:04.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:04.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:04.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:04.055][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:04.057][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-02 05:25:04.058][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 05:25:04.059][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:04.061][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:04.062][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-02 05:25:04.063][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-02 05:25:04.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-02 05:25:04.066][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:04.068][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:25:04.068][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:25:04.068][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:25:04.069][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 05:25:04.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:04.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:04.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:04.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:04.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:04.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:04.078][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:25:04.078][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-02 05:25:04.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:04.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:04.081][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:04.083][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-02 05:25:04.083][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-02 05:25:04.084][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:25:04.087][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:25:04.089][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-02 05:25:04.091][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:25:04.093][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:25:04.095][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:25:04.099][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-02 05:25:04.101][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-02 05:25:04.102][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-02 05:25:04.104][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-02 05:25:04.106][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:25:04.107][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:25:04.109][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-02 05:25:04.111][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-02 05:25:04.113][biodb::testThat]
biodb.INFO [2024-11-02 05:25:04.114][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-02 05:25:04.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:25:04.117][biodb::testThat]
biodb.DEBUG[2024-11-02 05:25:04.121][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-02 05:25:04.125][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:25:04.127][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-02 05:25:04.129][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:25:04.131][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-02 05:25:04.135][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-02 05:25:04.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:25:04.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:25:04.143][private$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[2024-11-02 05:25:04.874][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[2024-11-02 05:25:05.627][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:25:05.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-11-02 05:25:05.635][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-11-02 05:25:05.645][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 05:25:05.647][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-02 05:25:05.648][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-02 05:25:05.649][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 05:25:05.651][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:05.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:05.653][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:05.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:05.655][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-02 05:25:05.674][biodb::testContext]
biodb.INFO [2024-11-02 05:25:05.675][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:25:05.676][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-02 05:25:05.678][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 05:25:05.679][biodb::testContext]
biodb.INFO [2024-11-02 05:25:05.682][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:25:05.684][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 05:25:05.688][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:25:05.690][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 05:25:05.691][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 05:25:05.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.696][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 05:25:05.697][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 05:25:05.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.704][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 05:25:05.706][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 05:25:05.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.711][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 05:25:05.713][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 05:25:05.714][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 05:25:05.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.718][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[2024-11-02 05:25:05.719][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 05:25:05.721][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 05:25:05.722][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 05:25:05.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.727][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 05:25:05.729][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 05:25:05.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.733][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[2024-11-02 05:25:05.734][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 05:25:05.736][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 05:25:05.737][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 05:25:05.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.742][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 05:25:05.744][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 05:25:05.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.749][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 05:25:05.751][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 05:25:05.752][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 05:25:05.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.758][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:25:05.759][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 05:25:05.760][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 05:25:05.762][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 05:25:05.763][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 05:25:05.765][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 05:25:05.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.770][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 05:25:05.772][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 05:25:05.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.777][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 05:25:05.778][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 05:25:05.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.783][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 05:25:05.785][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 05:25:05.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.790][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 05:25:05.791][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 05:25:05.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.796][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 05:25:05.798][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 05:25:05.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.803][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 05:25:05.805][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 05:25:05.810][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 05:25:05.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.815][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 05:25:05.817][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 05:25:05.818][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 05:25:05.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:05.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:05.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:05.824][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 05:25:05.826][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.828][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-02 05:25:05.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.831][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:05.832][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.834][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.835][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.836][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.838][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:25:05.839][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:05.841][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.842][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 05:25:05.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:05.845][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.846][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.848][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:25:05.848][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:25:05.848][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:25:05.848][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:25:05.848][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:25:05.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:05.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:05.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.857][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.859][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:05.861][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:05.863][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.864][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.866][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 05:25:05.869][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.870][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:25:05.871][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.873][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:05.874][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.880][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:25:05.881][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:05.883][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.884][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 05:25:05.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:05.887][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.889][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.890][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:25:05.890][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:25:05.890][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:25:05.890][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 05:25:05.890][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 05:25:05.891][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:05.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.896][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:05.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.900][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.901][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.902][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:05.904][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:05.905][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.906][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.916][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 05:25:05.918][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.920][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-02 05:25:05.921][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.922][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:05.924][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.925][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.926][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.928][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.929][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 05:25:05.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:05.932][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.933][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 05:25:05.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:05.936][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.937][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.939][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.940][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:05.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.944][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:05.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.948][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.949][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.951][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:05.952][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:05.954][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.955][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.957][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 05:25:05.959][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.961][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 05:25:05.962][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:05.965][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.967][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.968][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.970][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.971][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 05:25:05.973][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:05.974][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.976][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 05:25:05.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:05.979][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:05.981][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 05:25:05.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.987][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:05.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:05.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:05.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:05.993][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:05.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:05.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:05.997][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:05.998][self$setPropertyValue]
biodb.DEBUG[2024-11-02 05:25:06.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:25:06.001][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.003][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[2024-11-02 05:25:06.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.009][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[2024-11-02 05:25:06.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.035][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[2024-11-02 05:25:06.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.094][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[2024-11-02 05:25:06.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.115][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 05:25:06.117][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 05:25:06.119][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 05:25:06.122][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 05:25:06.124][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:25:06.126][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 05:25:06.128][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 05:25:06.130][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 05:25:06.132][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 05:25:06.134][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 05:25:06.136][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:25:06.138][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 05:25:06.140][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 05:25:06.143][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 05:25:06.145][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 05:25:06.154][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 05:25:06.156][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 05:25:06.158][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 05:25:06.160][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:25:06.162][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 05:25:06.165][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 05:25:06.167][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 05:25:06.169][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 05:25:06.171][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 05:25:06.173][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 05:25:06.175][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 05:25:06.177][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 05:25:06.179][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 05:25:06.181][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 05:25:06.183][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 05:25:06.185][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 05:25:06.187][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 05:25:06.189][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 05:25:06.192][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 05:25:06.194][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 05:25:06.196][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 05:25:06.198][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 05:25:06.200][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 05:25:06.202][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 05:25:06.204][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 05:25:06.206][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 05:25:06.208][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 05:25:06.210][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 05:25:06.212][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 05:25:06.214][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 05:25:06.216][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 05:25:06.218][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 05:25:06.220][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 05:25:06.223][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 05:25:06.225][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 05:25:06.227][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 05:25:06.229][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 05:25:06.231][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 05:25:06.233][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 05:25:06.235][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 05:25:06.237][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 05:25:06.240][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 05:25:06.242][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 05:25:06.244][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 05:25:06.246][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 05:25:06.248][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 05:25:06.250][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 05:25:06.252][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 05:25:06.254][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 05:25:06.256][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 05:25:06.258][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 05:25:06.260][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:25:06.262][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:25:06.264][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 05:25:06.266][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 05:25:06.268][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 05:25:06.270][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 05:25:06.272][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 05:25:06.274][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 05:25:06.276][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 05:25:06.278][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 05:25:06.280][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 05:25:06.282][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 05:25:06.284][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 05:25:06.286][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 05:25:06.288][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 05:25:06.290][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 05:25:06.292][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 05:25:06.294][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 05:25:06.297][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 05:25:06.298][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 05:25:06.299][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.302][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.374][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.DEBUG[2024-11-02 05:25:06.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.391][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[2024-11-02 05:25:06.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.400][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[2024-11-02 05:25:06.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.409][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[2024-11-02 05:25:06.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.417][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[2024-11-02 05:25:06.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.435][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[2024-11-02 05:25:06.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 05:25:06.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.452][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[2024-11-02 05:25:06.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 05:25:06.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.461][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[2024-11-02 05:25:06.463][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-02 05:25:06.465][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-02 05:25:06.468][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:06.469][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 05:25:06.470][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:06.472][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 05:25:06.473][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:06.475][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 05:25:06.476][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:06.477][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-02 05:25:06.479][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 05:25:06.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 05:25:06.482][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:06.483][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-02 05:25:06.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-02 05:25:06.486][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-02 05:25:06.487][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 05:25:06.489][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 05:25:06.489][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 05:25:06.489][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 05:25:06.490][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 05:25:06.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:06.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:06.494][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 05:25:06.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 05:25:06.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 05:25:06.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 05:25:06.500][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:25:06.500][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-02 05:25:06.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 05:25:06.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 05:25:06.504][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 05:25:06.505][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-02 05:25:06.505][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-02 05:25:06.507][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 05:25:06.509][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 05:25:06.512][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-02 05:25:06.514][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 05:25:06.516][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 05:25:06.518][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 05:25:06.523][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-02 05:25:06.525][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-02 05:25:06.526][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-02 05:25:06.528][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-02 05:25:06.530][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:25:06.532][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 05:25:06.534][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-02 05:25:06.535][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-02 05:25:06.537][biodb::testThat]
biodb.INFO [2024-11-02 05:25:06.538][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-02 05:25:06.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 05:25:06.541][biodb::testThat]
biodb.DEBUG[2024-11-02 05:25:06.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-02 05:25:06.550][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:25:06.552][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-02 05:25:06.554][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:25:06.556][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-02 05:25:06.561][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[2024-11-02 05:25:06.565][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-02 05:25:06.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-02 05:25:06.569][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 05:25:06.571][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-02 05:25:06.577][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-02 05:25:06.579][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-02 05:25:06.581][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-02 05:25:06.583][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-02 05:25:06.585][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-02 05:25:06.586][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 05:25:06.588][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-02 05:25:06.589][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-02 05:25:06.591][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-02 05:25:06.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:25:06.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:06.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:06.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:06.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:06.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:06.608][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[2024-11-02 05:25:06.609][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-11-02 05:25:06.613][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-02 05:25:06.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-02 05:25:06.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-11-02 05:25:07.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-11-02 05:25:09.596][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-02 05:25:09.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-11-02 05:25:09.615][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-11-02 05:25:09.619][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-11-02 05:25:09.621][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-02 05:25:09.623][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-02 05:25:09.624][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-02 05:25:09.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 05:25:09.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:09.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:09.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:09.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:09.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:09.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 05:25:09.645][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.647][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.650][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.658][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:25:09.660][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:25:09.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.663][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.665][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-02 05:25:09.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-02 05:25:09.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.671][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:25:09.673][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:25:09.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.675][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.678][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 05:25:09.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 05:25:09.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.684][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 05:25:09.685][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 05:25:09.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.688][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.690][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 05:25:09.692][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 05:25:09.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.695][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.697][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:25:09.699][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:25:09.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.701][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:25:09.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 05:25:09.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.710][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:25:09.711][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:25:09.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.714][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-02 05:25:09.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-02 05:25:09.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.722][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:25:09.724][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:25:09.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.727][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:25:09.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 05:25:09.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.735][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:25:09.736][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:25:09.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.739][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 05:25:09.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 05:25:09.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.748][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:25:09.749][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:25:09.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.752][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.754][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-02 05:25:09.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-02 05:25:09.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.760][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:25:09.761][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:25:09.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.764][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.766][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 05:25:09.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 05:25:09.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:25:09.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:25:09.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:25:09.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:25:09.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 05:25:09.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 05:25:09.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 05:25:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 05:25:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 05:25:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 05:25:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 05:25:09.829][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-02 05:25:09.833][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 05:25:09.835][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-02 05:25:09.837][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-02 05:25:09.838][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 05:25:09.839][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 05:25:09.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 05:25:09.841][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 05:25:09.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 05:25:09.844][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 05:25:09.845][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
25.971 25.624 206.405
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.289 | 0.032 | 5.155 | |
| ChebiEntry | 0.212 | 0.002 | 0.217 | |