Pierrick Roger
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_18 |
| git_last_commit: 664af9c |
| git_last_commit_date: 2023-10-24 11:36:37 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:27 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 196/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.8.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.8.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings biodbChebi_1.8.0.tar.gz |
| StartedAt: 2023-11-02 08:44:05 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 08:48:35 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 270.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings biodbChebi_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbChebi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... 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-4.3.1/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2023-11-02 08:45:39.729][biodb::testContext]
biodb.INFO [2023-11-02 08:45:39.732][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:45:39.734][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-11-02 08:45:39.736][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:45:39.737][biodb::testContext]
biodb.INFO [2023-11-02 08:45:39.746][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:45:39.749][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:45:39.759][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:45:39.760][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:45:39.762][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:45:39.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.768][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:45:39.798][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:45:39.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.804][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:45:39.806][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:45:39.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.812][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:45:39.813][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:45:39.815][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:45:39.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.821][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:45:39.823][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:45:39.825][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:45:39.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.831][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:45:39.833][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:45:39.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.839][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:45:39.841][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:45:39.842][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:45:39.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.848][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:45:39.850][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:45:39.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.858][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:45:39.860][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:45:39.861][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:45:39.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.868][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:45:39.870][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:45:39.871][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:45:39.873][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:45:39.875][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:45:39.877][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:45:39.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.883][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:45:39.885][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:45:39.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.891][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:45:39.893][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:45:39.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.899][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:45:39.900][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:45:39.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.907][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:45:39.909][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:45:39.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.915][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:45:39.917][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:45:39.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.924][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:45:39.925][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:45:39.932][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:45:39.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.939][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:45:39.941][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:45:39.943][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:45:39.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:39.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:39.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:39.953][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:45:40.006][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.031][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-11-02 08:45:40.033][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:45:40.036][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.038][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.041][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.043][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:45:40.044][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:45:40.046][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.059][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:45:40.061][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:45:40.062][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.064][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.065][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:45:40.065][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:45:40.065][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:45:40.065][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:45:40.065][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:45:40.067][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:45:40.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:45:40.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.077][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:45:40.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:45:40.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.082][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.084][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:45:40.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.088][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:45:40.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.091][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:45:40.093][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.095][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.096][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.097][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.099][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:45:40.100][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:45:40.102][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.103][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:45:40.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:45:40.106][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.108][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.109][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:45:40.109][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:45:40.109][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:45:40.109][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:45:40.109][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:45:40.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:45:40.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:45:40.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.121][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:45:40.124][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:45:40.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.127][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.129][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:45:40.132][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.133][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-11-02 08:45:40.135][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.137][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:45:40.138][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.140][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.141][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.145][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:45:40.146][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:45:40.148][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.150][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:45:40.151][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:45:40.153][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.155][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.156][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.158][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:45:40.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:45:40.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.169][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:45:40.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:45:40.174][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.175][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.177][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:45:40.180][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.182][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:45:40.184][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.186][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:45:40.188][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.190][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.194][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.195][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:45:40.197][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:45:40.199][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.201][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:45:40.203][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:45:40.205][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.206][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.208][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:45:40.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:45:40.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.220][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.222][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.224][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:45:40.225][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:45:40.227][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.229][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:45:40.235][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:45:40.236][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.286][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.DEBUG[2023-11-02 08:45:40.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.293][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.DEBUG[2023-11-02 08:45:40.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.325][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[2023-11-02 08:45:40.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.370][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:45:40.377][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:45:40.380][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:45:40.383][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:45:40.385][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:45:40.388][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:45:40.390][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:45:40.394][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:45:40.396][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:45:40.399][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:45:40.401][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:45:40.404][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:45:40.406][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:45:40.408][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:45:40.411][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:45:40.413][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:45:40.415][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:45:40.418][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:45:40.420][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:45:40.422][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:45:40.425][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:45:40.427][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:45:40.429][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:45:40.432][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:45:40.434][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:45:40.436][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:45:40.439][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:45:40.441][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:45:40.444][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:45:40.447][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:45:40.449][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:45:40.452][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:45:40.455][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:45:40.457][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:45:40.460][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:45:40.462][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:45:40.464][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:45:40.467][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:45:40.469][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:45:40.472][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:45:40.474][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:45:40.477][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:45:40.479][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:45:40.482][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:45:40.484][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:45:40.487][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:45:40.489][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:45:40.491][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:45:40.494][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:45:40.497][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:45:40.499][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:45:40.502][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:45:40.514][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:45:40.517][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:45:40.520][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:45:40.522][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:45:40.525][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:45:40.527][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:45:40.530][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:45:40.532][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:45:40.535][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:45:40.537][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:45:40.540][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:45:40.542][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:45:40.545][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:45:40.547][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:45:40.549][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:45:40.551][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:45:40.554][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:45:40.556][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:45:40.558][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:45:40.561][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:45:40.563][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:45:40.565][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:45:40.567][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:45:40.569][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:45:40.571][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:45:40.574][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:45:40.576][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:45:40.578][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:45:40.580][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:45:40.583][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:45:40.585][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:45:40.594][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:45:40.597][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:45:40.602][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:45:40.603][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.606][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.631][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.DEBUG[2023-11-02 08:45:40.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.639][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.DEBUG[2023-11-02 08:45:40.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:40.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:45:40.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.769][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[2023-11-02 08:45:40.771][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-11-02 08:45:40.786][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-11-02 08:45:40.789][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.790][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.792][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:45:40.795][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.799][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.801][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-11-02 08:45:40.803][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-11-02 08:45:40.804][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:45:40.806][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.807][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-11-02 08:45:40.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-11-02 08:45:40.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-11-02 08:45:40.812][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:45:40.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:45:40.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:45:40.813][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:45:40.815][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-11-02 08:45:40.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:45:40.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:45:40.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:45:40.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:45:40.824][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:45:40.824][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-11-02 08:45:40.826][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:45:40.827][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:45:40.828][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:45:40.830][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-11-02 08:45:40.830][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-11-02 08:45:40.838][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:45:40.841][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:45:40.843][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-11-02 08:45:40.845][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:45:40.848][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:45:40.850][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:45:40.886][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-11-02 08:45:40.888][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-11-02 08:45:40.894][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-11-02 08:45:40.899][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-11-02 08:45:40.905][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:45:40.906][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:45:40.908][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-11-02 08:45:40.910][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-11-02 08:45:40.934][biodb::testThat]
biodb.INFO [2023-11-02 08:45:40.936][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-11-02 08:45:40.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:40.939][biodb::testThat]
biodb.TRACE[2023-11-02 08:45:40.945][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.3.1/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-11-02 08:45:40.948][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:45:40.953][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:45:40.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:45:40.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:40.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:40.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:40.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:40.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:40.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:45:41.003][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.005][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.008][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.034][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.036][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.039][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.085][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.090][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:41.099][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:41.100][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.102][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:41.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:41.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.110][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.111][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.114][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.122][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.123][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.125][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.126][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.128][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.134][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:45:41.136][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.139][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.141][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:45:41.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.147][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.148][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.151][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.159][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.163][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.170][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:45:41.172][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.173][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.174][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:45:41.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.181][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.183][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.184][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.185][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.187][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:41.303][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-11-02 08:45:41.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:41.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:45:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:45:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:45:41.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:45:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.381][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:45:41.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:45:41.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:45:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:45:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.531][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.533][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.535][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:41.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:41.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.576][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:41.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.620][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.622][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.624][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:41.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:41.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.661][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.662][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.663][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.665][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.666][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:41.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:41.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.700][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.702][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.703][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.704][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:41.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.742][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.744][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.745][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.746][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:41.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.767][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.773][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.778][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.784][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.785][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.786][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.788][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.789][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:41.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.808][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.814][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.826][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.827][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.829][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.830][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.831][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:41.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.851][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.857][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.863][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.870][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.872][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.873][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.875][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.894][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.906][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.912][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.913][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.914][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.916][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:41.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:41.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.992][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.993][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:41.996][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:41.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:41.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:42.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:42.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:42.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:42.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:42.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:42.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.035][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:42.036][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:42.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.039][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:42.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:42.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.059][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:42.061][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:42.062][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.064][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.073][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:42.075][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:42.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.077][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.086][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:42.088][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:42.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.091][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.100][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:42.102][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:42.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.105][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:42.116][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:42.117][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.118][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:42.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:42.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.132][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.141][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:42.143][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:42.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.145][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:42.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:42.157][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.159][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.168][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-11-02 08:45:42.170][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:42.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.172][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.182][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:42.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:42.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.186][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:42.195][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:42.197][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:42.198][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:42.200][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:45:42.215][biodb::testThat]
biodb.INFO [2023-11-02 08:45:42.217][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-11-02 08:45:42.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:42.219][biodb::testThat]
biodb.DEBUG[2023-11-02 08:45:42.242][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-11-02 08:45:42.252][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:45:42.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.INFO [2023-11-02 08:45:42.258][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-11-02 08:45:42.260][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:45:42.261][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:45:42.263][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:45:42.264][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:45:42.266][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:45:42.267][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:45:42.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:45:42.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:42.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:42.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:42.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:42.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:42.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:45:42.302][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
biodb.DEBUG[2023-11-02 08:45:42.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:45:42.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:45:42.336][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
biodb.TRACE[2023-11-02 08:45:43.459][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
biodb.DEBUG[2023-11-02 08:45:44.717][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:45:44.723][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.content"
biodb.TRACE[2023-11-02 08:45:44.747][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.request"
biodb.TRACE[2023-11-02 08:45:44.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml"
biodb.DEBUG[2023-11-02 08:45:44.753][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:45:44.789][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:45:44.791][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:45:44.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:45:44.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:45:44.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:45:44.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:45:44.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:45:44.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:45:44.811][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.TRACE[2023-11-02 08:45:44.817][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:44.819][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:44.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.822][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:44.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.874][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:44.876][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:44.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.878][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.880][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:45:44.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:45:44.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.886][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:44.888][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:44.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.890][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:45:44.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:45:44.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:44.900][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:44.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.902][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:44.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:44.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.910][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:44.912][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:44.913][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.914][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:44.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:44.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.922][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:44.924][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:44.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.926][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.928][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:44.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:45:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.934][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:45:44.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:44.937][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.938][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.940][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:45:44.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:44.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:44.948][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:44.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.950][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:44.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:44.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.958][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:44.960][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:44.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.962][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:44.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:44.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.970][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:45:44.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:44.973][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.975][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.976][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:45:44.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:45:44.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.982][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:44.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:44.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.987][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.989][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:45:44.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:45:44.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:44.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:44.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:44.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:44.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:45.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:45.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:45:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:45:45.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:45:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:45:45.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:45.052][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-11-02 08:45:45.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-11-02 08:45:45.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-11-02 08:45:45.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-11-02 08:45:45.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-11-02 08:45:45.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-11-02 08:45:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-11-02 08:45:45.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:45:45.085][biodb::testThat]
biodb.INFO [2023-11-02 08:45:45.086][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-11-02 08:45:45.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:45.089][biodb::testThat]
biodb.TRACE[2023-11-02 08:45:45.094][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:45.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:45.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.098][ef$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:45.101][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-11-02 08:45:45.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:45.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:45.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:45.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:45.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:45.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:45.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:45.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:45.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:45.174][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-11-02 08:45:45.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-11-02 08:45:45.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:45:45.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:45:45.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-11-02 08:45:47.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-11-02 08:45:48.463][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:45:48.466][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-11-02 08:45:48.471][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-11-02 08:45:48.476][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:45:48.480][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:45:48.482][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:45:48.484][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:45:49.637][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:45:50.814][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:45:50.817][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-11-02 08:45:50.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-11-02 08:45:50.826][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-11-02 08:45:50.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:50.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:50.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:50.856][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:50.858][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:50.859][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:50.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:50.862][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:45:50.895][biodb::testThat]
biodb.INFO [2023-11-02 08:45:50.900][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-11-02 08:45:50.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:50.904][biodb::testThat]
biodb.TRACE[2023-11-02 08:45:50.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:50.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:50.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:50.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:50.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:50.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:50.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:50.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:50.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:50.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:51.114][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:45:51.122][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:45:51.148][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:45:51.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:45:51.153][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-11-02 08:45:51.188][biodb::testThat]
biodb.INFO [2023-11-02 08:45:51.190][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-11-02 08:45:51.192][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:51.194][biodb::testThat]
biodb.TRACE[2023-11-02 08:45:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:51.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:51.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:51.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.273][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.279][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:45:51.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:45:51.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.285][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:45:51.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:45:51.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:51.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:51.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:45:51.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:45:51.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:45:51.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:51.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.365][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.372][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:45:51.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:45:51.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:45:51.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:51.384][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:45:51.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:45:51.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:51.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:45:51.401][biodb::testThat]
biodb.INFO [2023-11-02 08:45:51.402][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-11-02 08:45:51.404][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:51.405][biodb::testThat]
biodb.INFO [2023-11-02 08:45:51.419][biodb::testThat]
biodb.INFO [2023-11-02 08:45:51.421][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-11-02 08:45:51.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:51.424][biodb::testThat]
biodb.INFO [2023-11-02 08:45:51.439][biodb::testThat]
biodb.INFO [2023-11-02 08:45:51.440][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-11-02 08:45:51.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:51.443][biodb::testThat]
biodb.DEBUG[2023-11-02 08:45:51.449][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-11-02 08:45:52.600][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-11-02 08:45:57.459][biodb::testThat]
biodb.INFO [2023-11-02 08:45:57.461][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-11-02 08:45:57.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:57.463][biodb::testThat]
biodb.DEBUG[2023-11-02 08:45:58.490][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2023-11-02 08:45:59.535][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:59.537][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:59.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.540][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:59.543][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:45:59.544][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.546][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:45:59.548][biodb::testThat]
biodb.INFO [2023-11-02 08:45:59.550][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-11-02 08:45:59.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:45:59.553][biodb::testThat]
biodb.TRACE[2023-11-02 08:45:59.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:59.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:45:59.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:45:59.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:59.741][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:45:59.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:45:59.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:45:59.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:45:59.753][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-11-02 08:45:59.852][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:45:59.857][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:45:59.859][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:45:59.861][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:45:59.864][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-11-02 08:45:59.894][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:45:59.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:45:59.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:45:59.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:45:59.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:45:59.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:45:59.971][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:45:59.976][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:45:59.978][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:45:59.982][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:46:00.991][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:46:03.018][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:03.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-11-02 08:46:03.026][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-11-02 08:46:03.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:03.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:03.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:03.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:03.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:03.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:03.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:03.047][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-11-02 08:46:03.113][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:03.115][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-11-02 08:46:03.117][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:03.118][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:03.120][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:03.121][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:03.123][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:03.124][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:03.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:03.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:03.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:03.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:03.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:03.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:03.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:03.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-11-02 08:46:03.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:03.166][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:03.168][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-11-02 08:46:04.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-11-02 08:46:06.221][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:06.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-11-02 08:46:06.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-11-02 08:46:06.233][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-11-02 08:46:06.235][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:06.236][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:06.238][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:06.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:06.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:06.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:06.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:06.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:06.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:06.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:06.259][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.260][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.262][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.263][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.270][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:06.271][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:06.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.273][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.275][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:06.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.296][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:06.298][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:06.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.300][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:06.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:06.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.308][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:06.310][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:06.311][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.312][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:06.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:06.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:06.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:06.322][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.323][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:06.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:06.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.331][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:06.332][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:06.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.334][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.336][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:06.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.340][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:06.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.347][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:06.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:06.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.352][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:06.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.359][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:06.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:06.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.363][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:06.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:06.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.371][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:06.373][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:06.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.375][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.377][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:06.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:06.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.383][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:06.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:06.386][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.387][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.389][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:06.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:06.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:06.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:06.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:06.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:06.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:06.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:06.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:06.496][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-11-02 08:46:06.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:06.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:06.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:06.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:46:06.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:06.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:06.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:46:09.209][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:46:11.212][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:11.216][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-11-02 08:46:11.225][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-11-02 08:46:11.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:11.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:11.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:11.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:11.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:11.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:11.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:11.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:11.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:11.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:11.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:11.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:11.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:11.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:11.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:11.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:11.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:11.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:11.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:11.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:11.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:11.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:11.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:11.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:11.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:11.309][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2023-11-02 08:46:11.311][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:11.313][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2023-11-02 08:46:11.315][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:11.317][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:11.318][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:11.320][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:11.322][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:11.323][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:11.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:11.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:11.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:11.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:11.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:11.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:11.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:11.346][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2023-11-02 08:46:11.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:11.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:11.353][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2023-11-02 08:46:12.594][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2023-11-02 08:46:15.398][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:15.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2023-11-02 08:46:15.419][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2023-11-02 08:46:15.425][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2023-11-02 08:46:15.429][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:15.431][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:15.434][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:15.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:15.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:15.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:15.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:15.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:15.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:15.471][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.TRACE[2023-11-02 08:46:15.480][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.483][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.487][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.500][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:15.502][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:15.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.506][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.508][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:15.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:15.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.517][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:15.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:15.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.524][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:15.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:15.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.536][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:15.538][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:15.540][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.542][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:15.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:15.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:15.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:15.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.560][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:15.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:15.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.572][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:15.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:15.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.578][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.581][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:15.583][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.587][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.589][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:15.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.694][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:15.696][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:15.698][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.701][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:15.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:15.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.712][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:15.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:15.716][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.718][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:15.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.730][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:15.732][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:15.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.736][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.739][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:15.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.747][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:15.750][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:15.752][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.754][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:15.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:15.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:15.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:15.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:15.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:15.837][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2023-11-02 08:46:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:15.909][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:46:15.914][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:46:15.916][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:46:15.918][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:46:15.921][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-11-02 08:46:15.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:15.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:15.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:15.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:15.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:15.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:15.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:15.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:15.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:15.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:15.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:15.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:15.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:15.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:15.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:15.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:15.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:15.981][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-11-02 08:46:15.983][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:15.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-11-02 08:46:15.987][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:15.989][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:15.990][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:15.992][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:15.993][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:15.995][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:15.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:16.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:16.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:16.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:16.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:16.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:16.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:16.027][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-11-02 08:46:16.031][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:16.032][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:16.035][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-11-02 08:46:17.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-11-02 08:46:18.039][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:18.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-11-02 08:46:18.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-11-02 08:46:18.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-11-02 08:46:18.054][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:18.056][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:18.058][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:18.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:18.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:18.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:18.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:18.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:18.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:18.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:18.080][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.084][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.092][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:18.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:18.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.097][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.098][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:18.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:18.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.103][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:18.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:18.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.109][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.111][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:18.113][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:18.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.116][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:18.119][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:18.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.122][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.124][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:18.126][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.128][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.130][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:18.132][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:18.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.135][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.136][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:18.138][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:18.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.141][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:18.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:18.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.149][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:18.150][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:18.152][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.153][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.155][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:18.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:18.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.161][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:18.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:18.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.165][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:18.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:18.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:18.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:18.226][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-11-02 08:46:18.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:18.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:18.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:18.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:18.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:18.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:18.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:18.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:18.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:18.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:18.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:18.278][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-11-02 08:46:18.279][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:18.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-11-02 08:46:18.283][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:18.285][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:18.287][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:18.288][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:18.289][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:18.291][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:18.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:18.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:18.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:18.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:18.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:18.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:18.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:18.326][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-11-02 08:46:18.330][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:18.331][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:18.333][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-11-02 08:46:19.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-11-02 08:46:25.753][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:25.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-11-02 08:46:25.760][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-11-02 08:46:25.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-11-02 08:46:25.765][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:25.767][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:25.768][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:25.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:25.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:25.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:25.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:25.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:25.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:25.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:25.789][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.790][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.793][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.800][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:25.801][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:25.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.804][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.805][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:25.807][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:25.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.809][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.811][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:25.813][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:25.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.815][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.817][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:25.818][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:25.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.821][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.823][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:25.824][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:25.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.827][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.828][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:25.830][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.831][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.832][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.834][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:25.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:25.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.838][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.840][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:25.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:25.842][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.844][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:25.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:25.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.851][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:25.853][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:25.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.855][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:25.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:25.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.863][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:25.864][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:25.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.867][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:25.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:25.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:25.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:25.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:25.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:25.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:25.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:25.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:25.922][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-11-02 08:46:25.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:25.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:25.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:25.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:25.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:25.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:25.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:25.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:25.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:25.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:25.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:25.968][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-11-02 08:46:25.970][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:25.984][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-11-02 08:46:25.985][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:25.987][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:25.988][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:25.990][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:25.991][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:25.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:25.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:25.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:25.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:26.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:26.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:26.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:26.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:26.013][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-11-02 08:46:26.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:26.019][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:26.020][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-11-02 08:46:27.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-11-02 08:46:28.023][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:28.026][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-11-02 08:46:28.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-11-02 08:46:28.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-11-02 08:46:28.036][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:28.038][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:28.040][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:28.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:28.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:28.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:28.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:28.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:28.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:28.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:28.062][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.067][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.074][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:28.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:28.077][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.078][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.080][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:28.081][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:28.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.084][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.086][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:28.087][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:28.089][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.090][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.092][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:28.093][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:28.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.096][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.097][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:28.099][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:28.100][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.102][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.103][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:28.105][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.106][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.107][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.109][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:28.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:28.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.113][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.115][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:28.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:28.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.119][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:28.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:28.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.127][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:28.129][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:28.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.131][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.133][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:28.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:28.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.139][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:28.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:28.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.143][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:28.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:28.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:28.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:28.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:28.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:28.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:28.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:28.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:28.200][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-11-02 08:46:28.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:28.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:28.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:28.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:28.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:28.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:28.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:28.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:28.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:28.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:28.259][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-11-02 08:46:28.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:28.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-11-02 08:46:28.264][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:28.266][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:28.267][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:28.269][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:28.270][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:28.271][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:28.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:28.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:28.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:28.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:28.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:28.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:28.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:28.292][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-11-02 08:46:28.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:28.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:28.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-11-02 08:46:29.304][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-11-02 08:46:30.298][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:30.301][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-11-02 08:46:30.306][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-11-02 08:46:30.309][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-11-02 08:46:30.311][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:30.313][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:30.315][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:30.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:30.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:30.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:30.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:30.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:30.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:30.333][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.TRACE[2023-11-02 08:46:30.336][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.340][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.347][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:30.348][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:30.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.351][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.353][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:30.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:30.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.358][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:30.360][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:30.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.362][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:30.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:30.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.370][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:30.371][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:30.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.374][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:30.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:30.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.381][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:30.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:30.383][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.385][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:30.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:30.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.392][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:30.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:30.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.396][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.397][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:30.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:30.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.403][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:30.404][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.407][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.408][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:30.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:30.415][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:30.417][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.418][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:30.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:30.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.425][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:30.426][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:30.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.429][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:30.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:30.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.437][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:30.438][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:30.439][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.441][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.442][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.448][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:30.449][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:30.450][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.452][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:30.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:30.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:30.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:30.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:30.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:30.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:30.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:30.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:30.528][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-11-02 08:46:30.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:30.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:30.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:30.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:30.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:30.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:30.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:30.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:30.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:30.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:30.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:30.564][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-11-02 08:46:30.565][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:30.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-11-02 08:46:30.570][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:30.571][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:30.573][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:30.574][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:30.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:30.577][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:30.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:30.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:30.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:30.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:30.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:30.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:30.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:30.599][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-11-02 08:46:30.603][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:30.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:30.606][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-11-02 08:46:31.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-11-02 08:46:32.638][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:32.641][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-11-02 08:46:32.645][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-11-02 08:46:32.648][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-11-02 08:46:32.650][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:32.652][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:32.653][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:32.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:32.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:32.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:32.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:32.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:32.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:32.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:32.674][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.675][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.676][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.678][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.685][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:32.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:32.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.689][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.690][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:32.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:32.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.696][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:32.697][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:32.698][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.699][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.701][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:32.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:32.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.707][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:32.709][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:32.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.711][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:32.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:32.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.718][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:32.720][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:32.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.722][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.729][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:32.731][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:32.732][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.733][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.735][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:32.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:32.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.740][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:32.742][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.743][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.744][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.746][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:32.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.751][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:32.753][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:32.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.755][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:32.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:32.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.763][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:32.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:32.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.767][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:32.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:32.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.774][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:32.775][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:32.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.778][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.779][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:32.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:32.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.797][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:32.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:32.799][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.801][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.802][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:32.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:32.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:32.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:32.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:32.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:32.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:32.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:32.862][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-11-02 08:46:32.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:32.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:32.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:32.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:32.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:32.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:32.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:32.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:32.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:32.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:32.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:32.896][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-11-02 08:46:32.897][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:32.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-11-02 08:46:32.901][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:32.903][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:32.904][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:32.905][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:32.907][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:32.908][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:32.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:32.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:32.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:32.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:32.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:32.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:32.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:32.929][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-11-02 08:46:32.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:32.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:32.936][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-11-02 08:46:33.934][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-11-02 08:46:37.227][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:37.230][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-11-02 08:46:37.235][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-11-02 08:46:37.239][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-11-02 08:46:37.241][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:37.242][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:37.244][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:37.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:37.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:37.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:37.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:37.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:37.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:37.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:37.266][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.270][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.277][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:37.279][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:37.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.282][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.283][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.289][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:37.291][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:37.292][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.293][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:37.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:37.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.301][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:37.302][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:37.304][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.305][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:37.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:37.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.313][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:37.315][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:37.316][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.317][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:37.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.325][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:37.327][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:37.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.329][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.344][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:37.345][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.348][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:37.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:37.357][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:37.358][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.359][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:37.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:37.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.367][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:37.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:37.370][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.371][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:37.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:37.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.379][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:37.381][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:37.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.384][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.385][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:37.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:37.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.392][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:37.394][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:37.395][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.397][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.399][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:37.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:37.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:37.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:37.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:37.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:37.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:37.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:37.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:37.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:37.464][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-11-02 08:46:37.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:37.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:37.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:37.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:37.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:37.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:37.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:37.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:37.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:37.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:37.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:37.500][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-11-02 08:46:37.501][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:37.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-11-02 08:46:37.505][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:37.507][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:37.508][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:37.510][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:37.511][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:37.512][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:37.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:37.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:37.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:37.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:37.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:37.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:37.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:37.534][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-11-02 08:46:37.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:37.539][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:37.541][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-11-02 08:46:38.558][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-11-02 08:46:39.556][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:39.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-11-02 08:46:39.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-11-02 08:46:39.566][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-11-02 08:46:39.568][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:39.569][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:39.571][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:39.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:39.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:39.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:39.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:39.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:39.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:39.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:39.591][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.593][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.595][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.602][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:39.604][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:39.605][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.606][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.608][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:39.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.626][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:39.628][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:39.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.630][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:39.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:39.645][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:39.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.648][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:39.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:39.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.656][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:39.657][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:39.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.660][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:39.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:39.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.668][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:39.670][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:39.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.672][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.674][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:39.676][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.679][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.680][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:39.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.686][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:39.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:39.689][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.691][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:39.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:39.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.698][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:39.700][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:39.701][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.703][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:39.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:39.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.711][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:39.712][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:39.713][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.715][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.717][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:39.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:39.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:39.724][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:39.725][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.727][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:39.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:39.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:39.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:39.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:39.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:39.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:39.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:39.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:39.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:39.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:39.793][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-11-02 08:46:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:39.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:39.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:39.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:39.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:39.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:39.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:39.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:39.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:39.832][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-11-02 08:46:39.834][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:39.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-11-02 08:46:39.838][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:39.839][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:39.841][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:39.842][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:39.844][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:39.845][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:39.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:39.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:39.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:39.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:39.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:39.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:39.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:39.867][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-11-02 08:46:39.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:39.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:39.875][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-11-02 08:46:41.632][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-11-02 08:46:49.122][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:49.126][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-11-02 08:46:49.131][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-11-02 08:46:49.135][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-11-02 08:46:49.154][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:49.156][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:49.158][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:49.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:49.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:49.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:49.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:49.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:49.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:49.177][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.TRACE[2023-11-02 08:46:49.181][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.182][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.185][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.192][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:49.194][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:49.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.196][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.198][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:49.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:49.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.204][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:49.205][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:49.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.208][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.210][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:49.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:49.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.215][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:49.218][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:49.219][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.221][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:49.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:49.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.228][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:49.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:49.231][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.232][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:49.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:49.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.240][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:49.241][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:49.243][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.244][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.246][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:49.247][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.249][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.250][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.252][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.257][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:49.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:49.260][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.262][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:49.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:49.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.269][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:49.271][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:49.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.273][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:49.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:49.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.281][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:49.283][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:49.284][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.285][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.287][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:49.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:49.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.293][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:49.294][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:49.296][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.297][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:49.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:49.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:49.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:49.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:49.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:49.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:49.361][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-11-02 08:46:49.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:49.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:49.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:49.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:49.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:49.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:49.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:49.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:49.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:49.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:49.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:49.396][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-11-02 08:46:49.397][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:49.399][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-11-02 08:46:49.401][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:49.402][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:49.404][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:49.405][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:49.407][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:49.416][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:49.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:49.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:49.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:49.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:49.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:49.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:49.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:49.439][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-11-02 08:46:49.443][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:49.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:49.446][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-11-02 08:46:50.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-11-02 08:46:52.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:52.847][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-11-02 08:46:52.855][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-11-02 08:46:52.859][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-11-02 08:46:52.861][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:52.863][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:52.865][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:52.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:52.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:52.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:52.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:52.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:52.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:52.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:52.896][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:52.898][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:52.899][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.900][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:52.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.908][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:52.910][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:52.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.913][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.915][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:52.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:52.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.920][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:52.922][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:52.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.925][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.927][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:52.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:52.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.932][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:52.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:52.935][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.937][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:52.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:52.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:52.946][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:52.947][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.949][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:52.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:52.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:52.958][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:52.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.961][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.962][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:52.964][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:52.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.967][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.968][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:52.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:52.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:52.976][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:52.977][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.978][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:52.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:52.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.986][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:52.987][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:52.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.990][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:52.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:52.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:52.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:52.998][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:52.999][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:53.001][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.002][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.010][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:53.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:53.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.016][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:53.018][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:53.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.020][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:53.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:53.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:53.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:53.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:53.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:53.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:53.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:53.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:53.084][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-11-02 08:46:53.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:53.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:53.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:53.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:53.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:53.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:53.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:53.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:53.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:53.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:53.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:53.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:53.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:53.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:53.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:53.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:53.163][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-11-02 08:46:53.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:53.167][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-11-02 08:46:53.169][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:53.170][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:53.172][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:53.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:53.175][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:53.176][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:53.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:53.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:53.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:53.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:53.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:53.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:53.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:53.198][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-11-02 08:46:53.201][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:53.203][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:53.206][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-11-02 08:46:54.200][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-11-02 08:46:55.454][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:55.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-11-02 08:46:55.461][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-11-02 08:46:55.465][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-11-02 08:46:55.467][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:55.468][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:55.470][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:55.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:55.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:55.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:55.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:55.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:55.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:55.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:55.491][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.492][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.495][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.503][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:55.504][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:55.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.507][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:55.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:55.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.515][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:55.516][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:55.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.519][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:55.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.528][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:55.529][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:55.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.532][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:55.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:55.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.539][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:55.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:55.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.543][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:55.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.551][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:55.552][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:55.554][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.555][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.557][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:55.558][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.561][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:55.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:55.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:55.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.573][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:55.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.580][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:55.582][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:55.583][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.584][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:55.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:55.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.592][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:55.593][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:55.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.596][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.597][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.603][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:55.605][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:55.606][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.607][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:55.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:55.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:55.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:55.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:55.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:55.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:55.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:55.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:55.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:55.683][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-11-02 08:46:55.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:55.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:55.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:55.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:55.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:55.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:55.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:55.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:55.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:55.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:55.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:55.720][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-11-02 08:46:55.721][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:55.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-11-02 08:46:55.726][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:55.727][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:55.729][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:55.731][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:55.732][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:55.734][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:55.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:55.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:55.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:55.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:55.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:55.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:55.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:55.755][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-11-02 08:46:55.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:55.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:55.762][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-11-02 08:46:56.763][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-11-02 08:46:57.743][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:57.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-11-02 08:46:57.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-11-02 08:46:57.756][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-11-02 08:46:57.757][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:46:57.759][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:57.761][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:46:57.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:57.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:57.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:57.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:57.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:57.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:57.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:57.785][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.786][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.789][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.796][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:57.798][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:57.799][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.801][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.802][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:46:57.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:46:57.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.808][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:57.809][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:57.811][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.812][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.814][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:57.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:46:57.821][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:46:57.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.823][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.825][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:46:57.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:46:57.828][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.830][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.831][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:57.833][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:57.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.835][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.837][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:57.838][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.842][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.844][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:46:57.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.849][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:57.851][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:57.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.853][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:57.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:57.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.861][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:57.862][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:57.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.865][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:57.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:57.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.872][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:57.874][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:57.875][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.876][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.878][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:46:57.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:46:57.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.883][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:46:57.892][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:46:57.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.899][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:57.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:57.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:57.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:57.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:57.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:57.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:57.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:57.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:57.956][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-11-02 08:46:57.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:57.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:57.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:57.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:57.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:57.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:57.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:57.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:57.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:57.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:57.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:57.991][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-11-02 08:46:57.992][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:57.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-11-02 08:46:57.996][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:46:57.997][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:46:57.999][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:58.000][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:46:58.002][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:46:58.003][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:46:58.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:58.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:58.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:58.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:58.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:58.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:58.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:58.024][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-11-02 08:46:58.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:58.029][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:58.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-11-02 08:47:00.905][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-11-02 08:47:01.908][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:01.911][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-11-02 08:47:01.915][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-11-02 08:47:01.920][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-11-02 08:47:01.922][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:01.924][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:01.926][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:01.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:01.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:01.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:01.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:01.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:01.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:01.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:01.948][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:01.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:01.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.952][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:01.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:01.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.960][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:01.961][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:01.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.964][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:01.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.971][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:01.973][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:01.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.975][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:01.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:01.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.983][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:01.984][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:01.986][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.987][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.989][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:01.990][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:01.992][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.993][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:01.995][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:01.996][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:01.997][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:01.999][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.000][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:02.002][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.003][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.005][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.006][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:02.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.012][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:02.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:02.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.016][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:02.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:02.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.023][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:02.037][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:02.039][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.040][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.048][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:02.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:02.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.052][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.054][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:02.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:02.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.060][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:02.061][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:02.063][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.064][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:02.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:02.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:02.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:02.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:02.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:02.124][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-11-02 08:47:02.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:02.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:02.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:02.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:02.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:02.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:02.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:02.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:02.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:02.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:02.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:02.158][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-11-02 08:47:02.160][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:02.163][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-11-02 08:47:02.165][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:02.167][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:02.169][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:02.170][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:02.171][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:02.173][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:02.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:02.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:02.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:02.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:02.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:02.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:02.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:02.194][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-11-02 08:47:02.198][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:02.199][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:02.201][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-11-02 08:47:03.953][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-11-02 08:47:07.158][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:07.160][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-11-02 08:47:07.165][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-11-02 08:47:07.169][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-11-02 08:47:07.171][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:07.172][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:07.174][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:07.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:07.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:07.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:07.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:07.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:07.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:07.192][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[2023-11-02 08:47:07.195][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.197][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.198][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.200][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.207][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:07.209][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:07.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.211][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.219][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:07.221][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:07.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.223][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:07.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:07.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.231][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:07.232][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:07.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.235][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.243][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:07.244][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:07.246][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.247][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:07.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.268][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:07.269][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:07.271][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.272][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.274][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:07.275][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.277][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.278][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.280][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:07.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.286][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:07.287][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:07.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.290][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:07.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:07.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.298][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:07.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:07.301][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.302][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:07.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.310][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:07.311][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:07.313][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.314][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.322][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:07.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:07.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.327][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.329][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:07.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:07.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:07.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:07.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:07.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:07.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:07.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:07.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:07.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:07.393][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-11-02 08:47:07.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:07.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:07.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:07.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:07.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:07.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:07.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:07.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:07.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:07.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:07.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:07.430][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-11-02 08:47:07.432][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:07.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-11-02 08:47:07.436][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:07.438][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:07.439][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:07.441][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:07.442][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:07.444][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:07.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:07.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:07.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:07.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:07.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:07.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:07.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:07.466][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-11-02 08:47:07.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:07.472][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:07.474][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-11-02 08:47:08.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-11-02 08:47:11.045][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:11.048][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-11-02 08:47:11.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-11-02 08:47:11.055][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-11-02 08:47:11.057][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:11.059][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:11.060][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:11.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:11.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:11.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:11.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:11.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:11.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:11.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:11.081][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.085][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.105][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:11.107][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:11.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.110][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:11.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:11.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.118][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:11.119][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:11.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.122][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:11.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:11.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.130][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:11.132][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:11.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.134][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:11.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:11.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.142][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:11.144][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:11.145][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.147][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:11.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:11.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.154][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:11.156][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:11.157][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.159][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.160][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:11.162][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.165][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.167][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:11.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.173][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:11.174][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:11.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.177][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:11.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:11.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.185][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:11.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:11.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.190][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:11.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.198][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:11.200][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:11.201][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.202][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:11.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:11.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.210][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:11.212][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:11.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.215][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.216][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:11.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:11.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:11.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:11.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:11.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:11.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:11.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:11.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:11.281][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-11-02 08:47:11.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:11.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:11.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:11.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:11.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:11.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:11.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:11.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:11.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:11.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:11.317][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-11-02 08:47:11.319][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:11.321][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-11-02 08:47:11.323][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:11.324][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:11.326][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:11.327][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:11.329][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:11.330][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:11.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:11.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:11.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:11.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:11.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:11.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:11.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:11.352][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-11-02 08:47:11.355][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:11.357][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:11.359][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-11-02 08:47:12.382][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-11-02 08:47:14.243][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:14.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-11-02 08:47:14.264][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-11-02 08:47:14.268][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-11-02 08:47:14.271][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:14.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:14.275][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:14.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:14.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:14.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:14.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:14.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:14.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:14.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:14.296][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.301][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.309][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:14.311][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:14.312][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.313][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.315][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:14.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:14.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.321][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:14.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:14.324][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.326][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.327][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.333][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:14.335][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:14.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.338][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:14.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:14.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.345][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:14.347][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:14.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.350][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:14.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.358][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:14.359][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:14.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.362][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.364][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:14.366][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.368][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.370][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:14.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:14.378][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:14.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.381][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:14.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.389][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:14.390][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:14.392][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.393][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.401][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:14.403][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:14.404][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.405][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.407][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:14.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:14.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.413][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:14.415][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:14.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.417][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:14.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:14.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:14.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:14.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:14.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:14.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:14.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:14.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:14.486][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-11-02 08:47:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:14.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:14.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:14.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:14.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:14.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:14.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:14.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:14.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:14.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:14.522][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-11-02 08:47:14.524][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:14.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-11-02 08:47:14.536][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:14.538][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:14.540][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:14.541][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:14.543][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:14.544][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:14.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:14.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:14.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:14.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:14.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:14.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:14.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:14.566][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-11-02 08:47:14.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:14.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:14.573][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-11-02 08:47:15.574][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-11-02 08:47:19.761][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:19.764][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-11-02 08:47:19.769][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-11-02 08:47:19.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-11-02 08:47:19.774][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:19.775][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:19.777][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:19.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:19.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:19.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:19.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:19.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:19.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:19.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:19.799][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.800][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.803][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.810][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:19.812][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:19.813][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.814][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:19.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:19.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.822][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:19.823][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:19.824][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.826][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:19.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:19.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.833][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:19.835][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:19.836][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.837][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:19.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:19.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.844][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:19.846][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:19.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.848][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:19.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:19.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.856][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:19.857][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:19.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.860][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.862][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:19.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:19.864][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.866][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.867][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:19.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:19.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.873][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:19.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:19.876][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.877][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:19.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:19.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.885][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:19.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:19.887][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.889][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:19.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:19.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.896][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:19.898][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:19.899][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.901][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:19.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:19.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.908][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:19.909][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:19.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.912][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:19.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:19.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:19.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:19.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:19.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:19.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:19.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:19.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:19.987][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-11-02 08:47:19.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:19.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:19.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:19.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:19.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:19.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:19.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:20.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:20.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:20.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:20.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:20.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:20.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:20.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:20.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:20.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:20.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:20.023][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-11-02 08:47:20.024][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:20.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-11-02 08:47:20.028][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:20.030][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:20.031][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:20.033][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:20.034][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:20.036][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:20.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:20.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:20.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:20.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:20.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:20.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:20.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:20.057][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-11-02 08:47:20.061][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:20.062][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:20.064][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-11-02 08:47:21.057][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-11-02 08:47:22.050][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:22.053][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-11-02 08:47:22.057][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-11-02 08:47:22.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-11-02 08:47:22.063][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:22.065][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:22.066][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:22.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:22.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:22.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:22.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:22.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:22.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:22.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:22.087][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.089][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.091][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.099][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:22.100][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:22.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.103][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:22.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:22.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.110][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:22.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:22.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.115][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:22.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:22.124][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:22.125][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.127][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:22.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:22.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.134][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:22.136][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:22.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.139][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:22.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.146][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:22.148][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:22.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.150][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.152][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:22.154][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.155][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.156][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:22.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:22.166][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:22.167][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.168][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:22.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:22.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.176][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:22.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:22.179][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.180][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.182][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:22.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:22.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.188][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:22.190][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:22.191][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.193][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:22.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:22.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.200][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:22.202][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:22.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.204][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.206][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:22.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:22.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:22.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:22.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:22.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:22.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:22.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:22.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:22.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:22.283][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-11-02 08:47:22.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:22.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:22.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:22.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:22.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:22.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:22.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:22.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:22.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:22.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:22.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:22.319][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2023-11-02 08:47:22.321][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:22.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2023-11-02 08:47:22.325][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:22.326][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:22.328][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:22.330][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:22.331][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:22.332][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:22.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:22.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:22.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:22.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:22.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:22.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:22.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:22.354][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2023-11-02 08:47:22.358][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:22.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:22.361][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2023-11-02 08:47:23.361][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2023-11-02 08:47:24.602][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:24.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2023-11-02 08:47:24.610][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2023-11-02 08:47:24.613][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2023-11-02 08:47:24.615][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:24.617][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:24.618][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:24.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:24.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:24.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:24.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:24.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:24.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:24.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:24.639][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.644][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.651][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:24.652][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:24.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.655][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.657][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:24.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:24.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.663][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:24.665][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:24.667][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.668][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.670][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:24.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:24.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.676][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:24.678][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:24.679][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.680][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:24.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:24.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.688][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:24.689][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:24.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.692][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:24.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.699][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:24.700][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:24.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.703][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.705][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:24.706][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.709][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:24.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.716][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:24.718][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:24.719][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.720][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:24.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:24.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.728][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:24.729][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:24.743][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.744][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:24.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:24.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:24.754][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:24.755][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.756][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.758][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:24.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:24.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.764][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:24.765][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:24.767][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.768][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:24.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:24.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:24.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:24.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:24.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:24.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:24.834][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2023-11-02 08:47:24.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:24.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:24.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:24.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:24.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:24.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:24.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:24.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:24.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:24.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:24.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:24.874][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2023-11-02 08:47:24.875][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:24.877][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2023-11-02 08:47:24.883][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:24.886][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:24.888][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:24.889][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:24.891][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:24.893][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:24.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:24.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:24.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:24.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:24.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:24.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:24.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:24.918][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2023-11-02 08:47:24.923][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:24.924][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:24.927][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2023-11-02 08:47:28.727][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2023-11-02 08:47:30.652][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:30.655][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2023-11-02 08:47:30.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2023-11-02 08:47:30.663][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2023-11-02 08:47:30.665][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:30.667][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:30.669][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:30.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:30.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:30.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:30.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:30.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:30.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:30.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:30.692][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.694][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.696][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.697][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.705][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:30.707][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:30.709][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.710][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.712][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:30.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:30.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.718][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:30.720][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:30.722][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.723][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:30.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:30.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:30.733][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:30.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.736][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:30.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.765][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:30.767][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:30.768][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.770][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:30.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:30.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:30.779][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:30.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.782][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.784][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:30.786][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.787][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.789][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.790][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:30.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.797][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:30.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:30.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.802][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:30.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:30.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.810][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:30.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:30.813][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.815][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:30.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:30.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.823][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:30.824][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:30.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.827][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:30.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:30.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.836][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:30.837][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:30.839][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.840][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:30.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:30.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:30.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:30.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:30.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:30.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:30.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:30.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:30.911][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2023-11-02 08:47:30.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:30.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:30.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:30.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:30.966][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:30.971][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:30.973][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:47:30.974][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:30.977][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-11-02 08:47:30.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:30.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:30.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:30.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:30.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:30.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:30.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:30.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:31.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:31.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:31.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:31.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:31.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:31.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:31.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:31.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:31.825][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:31.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:31.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:31.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:47:32.828][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:47:33.822][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:33.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-11-02 08:47:33.830][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-11-02 08:47:33.835][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:33.839][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:33.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:33.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:47:34.848][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:47:35.855][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:35.858][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-11-02 08:47:35.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-11-02 08:47:35.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:35.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:35.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:35.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:35.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:35.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:35.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:35.885][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-11-02 08:47:35.887][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:35.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-11-02 08:47:35.891][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:35.892][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:35.894][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:35.895][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:35.897][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:35.898][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:35.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:35.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:35.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:35.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:35.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:35.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:35.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:35.920][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-11-02 08:47:35.924][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:35.925][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:35.927][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-11-02 08:47:36.965][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-11-02 08:47:37.988][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:37.991][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-11-02 08:47:37.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-11-02 08:47:38.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-11-02 08:47:38.002][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:38.003][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:38.005][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:38.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:38.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:38.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:38.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:38.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:38.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:38.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:38.027][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.030][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.031][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.038][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:38.040][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:38.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.043][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.044][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:38.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:38.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.050][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:38.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:38.053][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.055][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.057][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:38.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:38.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.063][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:38.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:38.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.067][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:38.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:38.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.074][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:38.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:38.077][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.079][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:38.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:38.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:38.088][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:38.089][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.091][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.093][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:38.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:38.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.098][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:38.100][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:38.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.103][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.105][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:38.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:38.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.132][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.135][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.142][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:38.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:38.145][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.146][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:38.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:38.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.155][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:38.156][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:38.157][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.159][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.160][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:38.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:38.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.166][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:38.168][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:38.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.170][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.172][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:38.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:38.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:38.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:38.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:38.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:38.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:38.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:38.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:38.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:38.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:38.237][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-11-02 08:47:38.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:38.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:38.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:38.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:38.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:38.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:38.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:38.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:38.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:38.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:38.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:38.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:38.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:38.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:38.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:38.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:38.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:38.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:38.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:38.310][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-11-02 08:47:38.311][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:38.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-11-02 08:47:38.315][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:38.317][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:38.319][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:38.320][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:38.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:38.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:38.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:38.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:38.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:38.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:38.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:38.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:38.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:38.346][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-11-02 08:47:38.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:38.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:38.353][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-11-02 08:47:39.372][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-11-02 08:47:40.355][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:40.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-11-02 08:47:40.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-11-02 08:47:40.368][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-11-02 08:47:40.370][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:40.372][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:40.374][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:40.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.405][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.TRACE[2023-11-02 08:47:40.408][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.410][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.413][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.420][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:40.422][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:40.423][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.425][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.427][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:40.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:40.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.432][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:40.434][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:40.435][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.437][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.438][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:40.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:40.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.444][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:40.446][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:40.447][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.449][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:40.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:40.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.456][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:40.458][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:40.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.460][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:40.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.468][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:40.470][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:40.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.472][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.474][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:40.476][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:40.477][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.478][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:40.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.486][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.490][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.498][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:40.499][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:40.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.502][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:40.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.509][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:40.511][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:40.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.513][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.515][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:40.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:40.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.521][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:40.522][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:40.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.525][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:40.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:40.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:40.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:40.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:40.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:40.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:40.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.591][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-11-02 08:47:40.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.644][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:40.649][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:40.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:47:40.653][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:40.654][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-11-02 08:47:40.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:40.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:40.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:40.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:40.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:40.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:40.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:40.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:40.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:40.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:40.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.454][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:41.459][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:41.461][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-11-02 08:47:41.462][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:41.464][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-11-02 08:47:41.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:41.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:41.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:41.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:41.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:41.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:41.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:41.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:41.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:41.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:41.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:41.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.242][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:42.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:42.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:47:42.262][biodb::testThat]
biodb.INFO [2023-11-02 08:47:42.263][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-11-02 08:47:42.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:47:42.266][biodb::testThat]
biodb.TRACE[2023-11-02 08:47:42.271][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:47:42.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:47:42.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:42.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:42.329][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:42.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-11-02 08:47:42.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:42.335][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-11-02 08:47:42.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:42.378][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:42.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-11-02 08:47:42.381][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:42.384][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-11-02 08:47:42.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:42.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.458][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:47:42.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.488][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.489][private$selectFields]
biodb.TRACE[2023-11-02 08:47:42.491][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:42.501][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:42.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.506][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.509][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.512][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.513][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.514][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.517][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.523][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.524][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.556][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-11-02 08:47:42.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.591][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.592][private$selectFields]
biodb.TRACE[2023-11-02 08:47:42.593][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:42.595][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:42.596][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.597][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.599][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.600][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.602][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.603][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.605][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.606][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.607][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.611][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.617][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.618][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:42.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.637][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-11-02 08:47:42.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:42.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.668][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.669][private$selectFields]
biodb.TRACE[2023-11-02 08:47:42.671][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:42.672][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:42.673][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.675][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.678][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.679][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.682][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.685][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.686][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.688][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:42.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.691][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.692][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.693][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.695][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:42.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:42.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.714][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2023-11-02 08:47:42.715][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:47:42.716][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:47:42.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:42.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:42.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:42.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:42.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:42.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:42.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:42.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:42.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:42.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:42.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:42.859][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:42.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:42.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:42.869][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:47:43.860][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:47:46.002][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:46.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-11-02 08:47:46.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-11-02 08:47:46.014][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:46.018][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:46.019][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:46.022][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:47:47.511][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:47:48.530][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:48.533][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-11-02 08:47:48.539][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-11-02 08:47:48.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:48.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:48.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:48.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:48.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:48.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:48.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:48.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:48.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:48.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:48.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:48.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:48.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:48.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:48.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:48.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:48.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:48.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:48.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:48.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:48.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:48.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:48.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:48.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:48.706][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:47:48.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:48.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:48.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:48.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:48.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:48.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:48.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:48.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.774][private$selectFields]
biodb.TRACE[2023-11-02 08:47:48.775][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:48.776][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:48.778][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.781][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.783][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.785][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.786][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.789][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.792][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.793][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.798][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.799][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:48.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.819][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-11-02 08:47:48.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:48.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:48.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:48.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:48.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:48.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:48.837][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.TRACE[2023-11-02 08:47:48.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.911][private$selectFields]
biodb.TRACE[2023-11-02 08:47:48.912][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:48.913][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:48.915][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.918][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.919][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.921][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.923][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.925][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.927][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.929][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.944][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:48.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.948][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.950][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.952][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.972][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-11-02 08:47:48.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:48.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:48.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:48.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:48.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:48.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:48.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:48.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:48.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:48.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:48.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.002][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.003][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.005][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.006][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.007][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.009][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.010][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.013][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.018][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.020][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.021][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.025][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.027][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.028][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.047][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-11-02 08:47:49.048][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:47:49.050][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:47:49.063][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:49.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:49.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:47:49.075][biodb::testThat]
biodb.INFO [2023-11-02 08:47:49.076][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-11-02 08:47:49.078][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:47:49.079][biodb::testThat]
biodb.TRACE[2023-11-02 08:47:49.083][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:47:49.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:47:49.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:49.143][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:49.148][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:49.150][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-11-02 08:47:49.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:49.153][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-11-02 08:47:49.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.192][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:49.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:49.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-11-02 08:47:49.200][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:49.202][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-11-02 08:47:49.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.273][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:47:49.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.304][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.305][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.306][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.308][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.309][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.310][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.312][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.313][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.314][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.316][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.319][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.320][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.323][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.326][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.327][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.329][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.331][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.350][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-11-02 08:47:49.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.381][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.382][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.384][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.385][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.391][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.400][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.404][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.405][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.408][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.411][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.413][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.415][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.432][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-11-02 08:47:49.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.463][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.464][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.465][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.466][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.468][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.469][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.472][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.473][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.477][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.478][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.480][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.481][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.483][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.484][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.485][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.487][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.504][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2023-11-02 08:47:49.506][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:47:49.507][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:47:49.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:49.565][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:49.570][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:49.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-11-02 08:47:49.573][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:49.575][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-11-02 08:47:49.579][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:49.583][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:49.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-11-02 08:47:49.587][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:49.589][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-11-02 08:47:49.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:49.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:49.702][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:47:49.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.734][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.736][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.738][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.739][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.742][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.744][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.745][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.751][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.756][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.758][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.759][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.760][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.779][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-11-02 08:47:49.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.795][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.TRACE[2023-11-02 08:47:49.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.808][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.809][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.811][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.812][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.813][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.815][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.816][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.817][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.819][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.820][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.823][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.824][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.827][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.830][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.831][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.833][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.834][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.853][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-11-02 08:47:49.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:49.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:49.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:49.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:49.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:49.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:49.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:49.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.882][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.883][private$selectFields]
biodb.TRACE[2023-11-02 08:47:49.885][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:49.886][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:49.887][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.892][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.893][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.907][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:49.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.913][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.914][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.916][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.917][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:49.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:49.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.936][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-11-02 08:47:49.937][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:47:49.938][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:47:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:47:49.965][biodb::testThat]
biodb.INFO [2023-11-02 08:47:49.966][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-11-02 08:47:49.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:47:49.969][biodb::testThat]
biodb.TRACE[2023-11-02 08:47:49.973][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:47:49.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:47:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:49.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:49.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:50.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:50.029][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:50.031][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-11-02 08:47:50.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:50.035][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-11-02 08:47:50.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.072][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:50.077][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:50.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-11-02 08:47:50.080][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:50.082][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-11-02 08:47:50.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.162][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:47:50.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.193][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.194][private$selectFields]
biodb.TRACE[2023-11-02 08:47:50.195][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:50.197][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:50.198][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.199][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.201][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.202][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.203][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.208][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.209][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.210][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.212][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.215][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.216][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.217][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.219][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:50.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.237][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-11-02 08:47:50.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.266][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.267][private$selectFields]
biodb.TRACE[2023-11-02 08:47:50.268][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:50.270][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:50.271][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.274][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.276][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.282][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.283][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.284][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.288][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.290][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.291][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.309][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-11-02 08:47:50.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.339][private$selectFields]
biodb.TRACE[2023-11-02 08:47:50.341][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:50.342][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:50.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.345][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.346][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.350][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.351][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.355][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.357][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.358][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.359][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.361][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.363][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.365][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:50.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.383][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2023-11-02 08:47:50.384][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:47:50.385][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:47:50.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:50.474][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:50.479][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:50.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-11-02 08:47:50.482][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:50.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-11-02 08:47:50.488][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:47:50.492][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:47:50.494][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-11-02 08:47:50.495][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:47:50.497][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-11-02 08:47:50.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:50.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:50.602][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:47:50.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.632][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.633][private$selectFields]
biodb.TRACE[2023-11-02 08:47:50.635][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:50.636][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:50.637][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.643][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.646][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.648][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.650][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.660][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.662][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.663][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.665][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.666][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.668][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:50.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.686][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-11-02 08:47:50.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.715][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.716][private$selectFields]
biodb.TRACE[2023-11-02 08:47:50.717][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:50.718][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:50.720][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.721][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.723][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.724][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.725][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.726][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.728][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.730][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.733][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.734][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.736][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.737][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.738][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.740][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.759][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-11-02 08:47:50.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:50.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.787][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.789][private$selectFields]
biodb.TRACE[2023-11-02 08:47:50.790][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:47:50.791][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:47:50.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.798][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.799][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.801][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.803][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.805][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.806][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-11-02 08:47:50.807][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.809][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.811][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.813][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-11-02 08:47:50.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:50.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:50.831][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-11-02 08:47:50.832][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:47:50.833][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:47:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:47:50.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:50.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:47:50.879][biodb::testThat]
biodb.INFO [2023-11-02 08:47:50.880][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-11-02 08:47:50.881][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:47:50.883][biodb::testThat]
biodb.DEBUG[2023-11-02 08:47:50.885][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-11-02 08:47:50.887][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:47:50.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-11-02 08:47:50.890][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:47:50.892][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:50.893][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:50.895][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:50.905][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:50.906][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:50.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:50.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:50.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:50.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:50.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:50.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:50.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:50.927][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-11-02 08:47:50.930][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:50.932][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:50.934][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-11-02 08:47:52.627][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-11-02 08:47:53.623][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:53.625][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-11-02 08:47:53.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-11-02 08:47:53.633][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-11-02 08:47:53.634][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:53.636][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:47:53.638][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:53.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:53.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:53.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:53.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:53.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:53.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:53.654][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.TRACE[2023-11-02 08:47:53.657][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.660][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.661][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.669][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:53.670][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:53.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.673][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.674][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:53.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:53.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.678][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:53.681][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:53.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.684][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.685][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:53.687][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:53.688][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.689][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:53.692][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:53.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.695][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.696][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:47:53.698][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:53.699][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.700][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.702][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:53.703][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:53.705][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.706][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.708][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:47:53.709][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:47:53.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.711][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.713][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:47:53.715][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:47:53.716][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.717][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:47:53.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:47:53.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.723][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:53.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:53.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:53.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:53.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:47:53.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:47:53.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:53.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:53.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:53.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:53.778][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-11-02 08:47:53.779][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-11-02 08:47:53.793][biodb::testThat]
biodb.INFO [2023-11-02 08:47:53.794][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-11-02 08:47:53.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:47:53.797][biodb::testThat]
biodb.DEBUG[2023-11-02 08:47:53.813][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-11-02 08:47:53.814][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-11-02 08:47:53.816][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-11-02 08:47:53.818][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-11-02 08:47:53.819][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-11-02 08:47:53.821][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:47:53.822][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:47:53.824][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:47:53.837][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:47:53.839][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:47:53.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:53.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:53.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:53.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:53.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:53.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:53.860][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.DEBUG[2023-11-02 08:47:53.862][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-11-02 08:47:53.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:53.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:53.869][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-11-02 08:47:54.853][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-11-02 08:47:55.855][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:55.858][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-11-02 08:47:55.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-11-02 08:47:55.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:55.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:55.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:55.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:55.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:55.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:55.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:55.880][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-11-02 08:47:55.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:55.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:55.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-11-02 08:47:56.880][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-11-02 08:47:57.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:57.885][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-11-02 08:47:57.890][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-11-02 08:47:57.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:57.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:57.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:57.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:57.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:57.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:57.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:57.909][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-11-02 08:47:57.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:57.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:57.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-11-02 08:47:58.911][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-11-02 08:47:59.911][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:47:59.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-11-02 08:47:59.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-11-02 08:47:59.923][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-11-02 08:47:59.926][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:47:59.928][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-11-02 08:47:59.930][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-11-02 08:47:59.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:59.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:59.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:59.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:59.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:59.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:59.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:47:59.953][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:59.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:59.956][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.958][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:47:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:47:59.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.966][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:47:59.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:47:59.969][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.971][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.972][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:47:59.974][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:47:59.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.977][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.979][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:47:59.981][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:47:59.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.984][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.986][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:47:59.987][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:47:59.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.990][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.992][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:59.994][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:47:59.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:59.997][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:59.999][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:00.000][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:00.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.003][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.005][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.007][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.010][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.012][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:00.013][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:00.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.016][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.018][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:00.020][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:00.022][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.023][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.025][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:00.027][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:00.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.030][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:00.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:00.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:00.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:00.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:00.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:00.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:00.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:48:00.117][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.119][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.120][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.122][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.130][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:48:00.132][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:48:00.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.137][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.139][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:48:00.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:48:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.145][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:00.147][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:00.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.150][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.153][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:00.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.159][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:48:00.161][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:48:00.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.164][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:48:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:48:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.173][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.175][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.178][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.186][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.188][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.191][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.199][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:00.200][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:00.202][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.203][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:00.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:00.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.211][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.213][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.216][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.224][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:00.226][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:00.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.228][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:00.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:00.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.237][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:00.238][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:00.240][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.241][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:00.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.249][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:00.251][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:00.252][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.253][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:00.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:00.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:00.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:00.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:00.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:00.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:00.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:00.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:00.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:48:00.322][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.323][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.326][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.333][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:48:00.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:48:00.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.339][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.341][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:48:00.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:48:00.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.347][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:00.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:00.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.361][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:00.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:00.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.370][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:48:00.371][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:48:00.373][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.374][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:48:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:48:00.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.382][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.383][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.386][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:48:00.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.394][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.396][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.397][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.398][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.400][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:00.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.406][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:00.408][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:00.409][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.410][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.412][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:00.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:00.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.418][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.420][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.422][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:00.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.430][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:00.432][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:00.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.435][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:00.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:00.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.443][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:00.444][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:00.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.447][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.455][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:00.456][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:00.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.459][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:00.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:00.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:00.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:00.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:00.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:00.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:00.562][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-11-02 08:48:00.563][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-11-02 08:48:00.564][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-11-02 08:48:00.588][biodb::testThat]
biodb.INFO [2023-11-02 08:48:00.590][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-11-02 08:48:00.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:00.593][biodb::testThat]
biodb.INFO [2023-11-02 08:48:00.640][biodb::testThat]
biodb.INFO [2023-11-02 08:48:00.642][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-11-02 08:48:00.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:00.644][biodb::testThat]
biodb.INFO [2023-11-02 08:48:00.660][biodb::testThat]
biodb.INFO [2023-11-02 08:48:00.662][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-11-02 08:48:00.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:00.665][biodb::testThat]
biodb.DEBUG[2023-11-02 08:48:00.669][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:00.673][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:00.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:00.678][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:01.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:09.270][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:09.273][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-11-02 08:48:09.279][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-11-02 08:48:09.300][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:09.301][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:09.303][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:09.304][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:09.306][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:09.307][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:09.309][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:09.310][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:48:09.312][biodb::testThat]
biodb.INFO [2023-11-02 08:48:09.314][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-11-02 08:48:09.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:09.316][biodb::testThat]
biodb.ERROR[2023-11-02 08:48:09.340][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-11-02 08:48:09.368][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-11-02 08:48:09.389][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:48:09.391][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-11-02 08:48:09.392][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-11-02 08:48:09.394][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:48:09.395][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:09.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:09.397][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:09.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:09.400][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:48:09.417][biodb::testContext]
biodb.INFO [2023-11-02 08:48:09.418][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:48:09.420][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-11-02 08:48:09.421][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:48:09.423][biodb::testContext]
biodb.INFO [2023-11-02 08:48:09.425][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:48:09.428][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:48:09.433][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:09.434][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:48:09.436][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:48:09.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.441][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:48:09.443][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:48:09.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.448][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:48:09.450][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:48:09.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.455][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:48:09.456][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:48:09.458][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:48:09.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.478][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:48:09.479][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:48:09.481][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:48:09.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.486][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:48:09.488][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:48:09.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.493][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:48:09.494][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:48:09.496][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:48:09.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.501][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:48:09.503][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:48:09.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.508][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:48:09.510][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:48:09.511][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:48:09.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.516][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:48:09.518][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:48:09.519][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:48:09.521][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:48:09.523][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:48:09.524][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:48:09.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.530][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:48:09.532][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:48:09.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.537][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:48:09.539][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:48:09.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.544][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:48:09.546][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:48:09.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.551][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:48:09.553][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:48:09.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.558][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:48:09.560][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:48:09.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.565][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:48:09.566][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:48:09.572][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:48:09.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.577][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:48:09.579][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:48:09.580][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:48:09.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:09.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:09.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:09.586][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:48:09.589][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.591][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-11-02 08:48:09.592][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.594][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:09.595][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.597][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.598][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.600][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.601][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:48:09.603][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:09.604][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.606][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:48:09.607][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:09.609][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.610][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.612][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:09.612][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:09.612][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:09.612][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:48:09.612][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:48:09.613][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:09.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.617][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:09.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.622][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.623][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.625][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:09.626][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:09.627][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.629][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.631][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:48:09.633][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.635][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:48:09.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.638][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:09.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.645][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:48:09.646][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:09.648][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.649][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:48:09.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:09.652][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.655][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:09.655][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:09.655][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:09.655][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:48:09.655][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:48:09.657][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:09.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:09.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.665][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.666][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.668][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:09.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:09.670][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.672][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.674][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:48:09.676][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.678][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-11-02 08:48:09.679][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:09.682][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.684][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.685][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.686][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.688][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:48:09.689][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:09.691][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.693][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:48:09.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:09.696][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.699][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:09.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.703][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.704][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:09.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.710][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.711][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:09.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:09.714][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.716][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.717][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:48:09.720][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.721][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:48:09.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.724][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:09.965][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.966][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.968][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.969][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.971][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:48:09.972][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:09.973][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.975][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:48:09.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:09.978][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:09.981][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:09.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.987][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:09.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:09.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:09.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:09.993][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:09.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:09.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:09.997][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:09.998][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:10.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:10.002][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.016][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[2023-11-02 08:48:10.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.029][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[2023-11-02 08:48:10.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.069][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[2023-11-02 08:48:10.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.075][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[2023-11-02 08:48:10.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.094][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[2023-11-02 08:48:10.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.107][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[2023-11-02 08:48:10.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.115][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:48:10.117][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:48:10.119][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:48:10.121][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:48:10.123][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:48:10.125][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:48:10.127][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:48:10.129][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:48:10.131][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:48:10.133][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:48:10.136][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:48:10.138][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:48:10.140][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:48:10.142][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:48:10.144][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:48:10.146][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:48:10.149][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:48:10.151][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:48:10.153][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:48:10.155][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:48:10.157][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:48:10.159][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:48:10.161][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:48:10.163][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:48:10.165][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:48:10.167][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:48:10.169][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:48:10.171][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:48:10.173][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:48:10.175][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:48:10.177][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:48:10.179][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:48:10.181][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:48:10.183][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:48:10.184][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:48:10.186][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:48:10.188][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:48:10.190][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:48:10.192][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:48:10.194][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:48:10.196][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:48:10.198][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:48:10.200][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:48:10.202][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:48:10.204][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:48:10.206][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:48:10.208][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:48:10.210][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:48:10.212][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:48:10.214][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:48:10.223][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:48:10.225][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:48:10.227][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:48:10.229][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:48:10.231][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:48:10.233][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:48:10.235][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:48:10.237][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:48:10.239][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:48:10.241][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:48:10.243][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:48:10.245][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:48:10.247][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:48:10.249][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:48:10.251][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:48:10.253][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:48:10.255][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:48:10.257][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:48:10.259][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:48:10.261][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:48:10.264][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:48:10.266][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:48:10.268][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:48:10.270][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:48:10.272][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:48:10.274][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:48:10.276][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:48:10.278][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:48:10.280][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:48:10.282][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:48:10.284][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:48:10.286][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:48:10.288][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:48:10.291][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:48:10.293][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:48:10.294][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:10.295][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.298][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.391][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[2023-11-02 08:48:10.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.400][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[2023-11-02 08:48:10.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:10.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:10.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:10.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:10.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:10.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:10.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:10.462][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-11-02 08:48:10.465][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-11-02 08:48:10.468][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:10.469][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:48:10.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:10.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:10.474][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:10.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:10.478][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:10.479][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-11-02 08:48:10.481][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-11-02 08:48:10.482][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:10.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:10.494][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-11-02 08:48:10.496][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-11-02 08:48:10.498][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-11-02 08:48:10.500][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:10.501][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:10.501][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:10.501][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:10.503][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-11-02 08:48:10.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:10.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:10.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:10.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:10.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:10.512][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:10.514][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:48:10.514][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-11-02 08:48:10.515][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:10.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:10.519][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:10.520][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-11-02 08:48:10.520][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-11-02 08:48:10.522][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:48:10.525][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:48:10.527][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-11-02 08:48:10.529][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:48:10.532][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:48:10.534][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:48:10.539][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-11-02 08:48:10.540][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-11-02 08:48:10.542][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-11-02 08:48:10.544][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-11-02 08:48:10.546][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:48:10.548][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:48:10.550][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-11-02 08:48:10.551][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-11-02 08:48:10.553][biodb::testThat]
biodb.INFO [2023-11-02 08:48:10.554][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-11-02 08:48:10.556][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:10.557][biodb::testThat]
biodb.DEBUG[2023-11-02 08:48:10.563][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-11-02 08:48:10.567][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:10.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-11-02 08:48:10.571][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:10.574][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-11-02 08:48:10.579][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:10.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:10.585][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:10.587][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:14.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:15.616][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:15.619][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-11-02 08:48:15.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-11-02 08:48:15.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:15.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:15.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:15.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:15.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:15.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:15.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:15.667][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:15.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:15.673][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:15.675][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:16.668][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:17.657][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:17.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-11-02 08:48:17.665][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-11-02 08:48:17.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:17.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:17.727][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:17.732][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:17.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-11-02 08:48:17.736][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:17.737][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-11-02 08:48:17.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:17.770][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:17.775][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:17.776][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-11-02 08:48:17.778][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:17.780][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-11-02 08:48:17.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.797][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.DEBUG[2023-11-02 08:48:17.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:17.818][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:17.822][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:17.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-11-02 08:48:17.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:17.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-11-02 08:48:17.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:17.846][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:17.850][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:17.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-11-02 08:48:17.854][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:17.856][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-11-02 08:48:17.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:17.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:17.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:17.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:17.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:17.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:17.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:17.875][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:17.879][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:17.880][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:17.883][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:18.881][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:19.881][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:19.884][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-11-02 08:48:19.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-11-02 08:48:19.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:19.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:19.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:19.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:19.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:19.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:19.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:48:19.919][biodb::testThat]
biodb.INFO [2023-11-02 08:48:19.920][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-11-02 08:48:19.922][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:19.923][biodb::testThat]
biodb.DEBUG[2023-11-02 08:48:19.927][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:19.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:19.935][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:19.937][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:20.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:21.988][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:21.990][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-11-02 08:48:21.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-11-02 08:48:21.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:21.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:22.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:22.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:22.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:22.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:22.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:22.019][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:22.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:22.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:22.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:23.024][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:24.028][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:24.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-11-02 08:48:24.037][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-11-02 08:48:24.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:24.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:48:24.081][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:48:24.082][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-11-02 08:48:24.084][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-11-02 08:48:24.085][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:48:24.086][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.088][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.091][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:48:24.097][biodb::testContext]
biodb.INFO [2023-11-02 08:48:24.099][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:48:24.100][biodb::testContext] Test context - Test web services
biodb.INFO [2023-11-02 08:48:24.101][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:48:24.103][biodb::testContext]
biodb.INFO [2023-11-02 08:48:24.105][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:48:24.108][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:48:24.112][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:24.114][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:48:24.115][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:48:24.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.119][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[2023-11-02 08:48:24.120][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:48:24.122][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:48:24.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.127][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:48:24.128][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:48:24.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.133][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:48:24.134][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:48:24.136][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:48:24.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.141][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:48:24.142][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:48:24.144][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:48:24.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.149][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:48:24.150][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:48:24.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.155][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:48:24.157][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:48:24.158][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:48:24.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.163][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:48:24.164][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:48:24.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.169][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:48:24.170][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:48:24.172][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:48:24.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.177][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:48:24.178][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:48:24.180][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:48:24.181][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:48:24.182][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:48:24.184][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:48:24.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.189][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:48:24.190][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:48:24.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.195][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:48:24.197][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:48:24.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.201][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:48:24.203][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:48:24.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.208][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:48:24.209][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:48:24.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.214][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:48:24.216][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:48:24.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.221][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:48:24.222][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:48:24.227][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:48:24.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.232][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:48:24.234][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:48:24.235][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:48:24.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.240][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:48:24.243][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.244][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-11-02 08:48:24.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:24.249][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.250][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.251][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.254][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:48:24.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:24.257][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.258][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:48:24.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:24.261][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.262][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.264][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:24.264][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:24.264][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:24.264][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:48:24.264][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:48:24.265][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:24.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.269][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:24.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.274][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:24.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:24.278][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.279][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.281][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:48:24.284][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.285][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:48:24.286][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:24.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.291][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.293][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.295][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:48:24.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:24.298][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.299][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:48:24.308][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:24.310][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:24.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:24.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:24.313][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:48:24.313][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:48:24.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:24.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:24.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.323][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:24.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:24.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.328][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.329][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:48:24.332][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.333][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-11-02 08:48:24.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:24.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.339][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.340][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.341][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.343][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:48:24.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:24.346][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.347][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:48:24.348][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:24.350][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.353][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.354][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:24.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.358][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:24.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.363][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.365][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:24.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:24.367][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.368][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.370][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:48:24.373][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.374][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:48:24.375][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:24.378][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.380][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.383][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.384][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:48:24.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:24.387][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.388][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:48:24.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:24.391][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.392][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.393][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.395][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:24.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.399][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:24.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.403][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.404][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.405][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:24.407][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:24.408][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.409][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:24.411][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:24.412][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.457][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[2023-11-02 08:48:24.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.501][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[2023-11-02 08:48:24.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.521][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:48:24.523][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:48:24.525][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:48:24.527][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:48:24.529][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:48:24.531][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:48:24.532][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:48:24.534][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:48:24.536][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:48:24.538][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:48:24.540][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:48:24.542][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:48:24.551][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:48:24.553][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:48:24.555][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:48:24.557][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:48:24.559][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:48:24.561][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:48:24.563][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:48:24.565][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:48:24.567][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:48:24.569][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:48:24.571][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:48:24.573][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:48:24.575][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:48:24.577][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:48:24.579][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:48:24.580][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:48:24.582][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:48:24.584][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:48:24.586][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:48:24.588][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:48:24.590][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:48:24.592][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:48:24.594][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:48:24.596][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:48:24.598][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:48:24.600][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:48:24.601][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:48:24.603][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:48:24.605][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:48:24.607][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:48:24.609][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:48:24.611][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:48:24.613][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:48:24.615][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:48:24.617][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:48:24.619][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:48:24.621][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:48:24.623][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:48:24.625][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:48:24.627][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:48:24.630][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:48:24.632][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:48:24.634][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:48:24.636][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:48:24.638][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:48:24.640][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:48:24.642][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:48:24.644][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:48:24.646][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:48:24.648][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:48:24.650][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:48:24.652][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:48:24.654][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:48:24.656][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:48:24.658][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:48:24.660][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:48:24.662][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:48:24.664][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:48:24.666][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:48:24.668][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:48:24.670][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:48:24.672][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:48:24.673][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:48:24.675][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:48:24.677][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:48:24.679][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:48:24.681][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:48:24.683][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:48:24.685][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:48:24.687][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:48:24.689][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:48:24.691][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:48:24.693][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:48:24.695][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:24.696][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.698][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.769][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[2023-11-02 08:48:24.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.830][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.DEBUG[2023-11-02 08:48:24.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:24.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:24.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:24.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:24.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:24.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:24.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:24.859][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-11-02 08:48:24.860][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-11-02 08:48:24.863][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.865][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.866][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.867][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:24.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.870][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.872][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.873][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-11-02 08:48:24.874][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-11-02 08:48:24.876][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:24.877][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.879][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-11-02 08:48:24.880][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-11-02 08:48:24.882][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-11-02 08:48:24.883][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:24.884][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:24.884][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:24.884][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:24.886][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-11-02 08:48:24.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.892][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:24.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:24.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:24.896][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:24.897][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:48:24.897][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-11-02 08:48:24.899][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:24.900][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:24.901][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:24.903][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-11-02 08:48:24.903][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-11-02 08:48:24.905][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:48:24.907][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:48:24.909][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-11-02 08:48:24.911][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:48:24.914][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:48:24.916][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:48:24.921][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-11-02 08:48:24.922][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-11-02 08:48:24.924][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-11-02 08:48:24.926][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-11-02 08:48:24.928][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:48:24.929][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:48:24.931][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-11-02 08:48:24.933][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-11-02 08:48:24.935][biodb::testThat]
biodb.INFO [2023-11-02 08:48:24.936][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-11-02 08:48:24.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:24.939][biodb::testThat]
biodb.DEBUG[2023-11-02 08:48:24.943][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-11-02 08:48:24.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:24.950][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-11-02 08:48:24.952][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:24.954][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-11-02 08:48:24.958][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:24.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:24.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:24.966][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-11-02 08:48:25.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-11-02 08:48:26.948][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:26.950][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-11-02 08:48:26.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-11-02 08:48:26.967][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:48:26.969][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-11-02 08:48:26.970][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-11-02 08:48:26.972][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:48:26.973][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:26.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:26.975][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:26.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:26.977][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:26.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:48:26.984][biodb::testContext]
biodb.INFO [2023-11-02 08:48:26.986][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:48:26.987][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-11-02 08:48:26.988][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:48:26.990][biodb::testContext]
biodb.INFO [2023-11-02 08:48:26.992][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:48:26.994][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:48:26.999][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:27.000][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:48:27.002][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:48:27.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.007][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:48:27.008][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:48:27.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.013][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:48:27.015][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:48:27.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.031][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:48:27.033][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:48:27.034][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:48:27.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.039][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:48:27.040][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:48:27.042][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:48:27.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.047][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:48:27.048][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:48:27.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.051][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[2023-11-02 08:48:27.053][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:48:27.054][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:48:27.055][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:48:27.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.060][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:48:27.062][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:48:27.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.066][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:48:27.068][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:48:27.069][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:48:27.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.074][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:48:27.075][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:48:27.077][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:48:27.078][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:48:27.079][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:48:27.082][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:48:27.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.085][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[2023-11-02 08:48:27.086][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:48:27.088][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:48:27.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.093][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:48:27.094][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:48:27.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.099][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:48:27.100][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:48:27.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.105][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:48:27.107][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:48:27.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.112][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:48:27.113][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:48:27.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.118][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:48:27.119][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:48:27.124][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:48:27.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.129][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:48:27.130][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:48:27.131][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:48:27.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.136][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:48:27.139][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.140][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-11-02 08:48:27.142][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.143][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:27.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.146][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.147][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.150][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:48:27.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:27.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.154][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:48:27.155][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:27.156][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.158][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.159][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:27.159][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:27.159][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:27.159][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:48:27.159][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:48:27.160][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:27.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.164][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:27.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.169][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:27.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:27.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.174][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.176][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:48:27.178][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.180][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:48:27.181][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.183][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:27.184][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.185][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.187][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.188][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.189][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:48:27.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:27.192][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.193][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:48:27.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:27.196][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.198][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.199][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:27.199][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:27.199][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:27.199][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:48:27.199][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:48:27.200][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:27.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:27.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.208][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.209][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.211][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:27.212][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:27.213][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.214][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.216][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:48:27.219][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.220][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-11-02 08:48:27.221][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:27.224][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.225][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.228][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.229][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:48:27.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:27.232][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.234][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:48:27.235][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:27.236][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.238][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.239][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:27.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.244][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:27.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.249][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:27.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:27.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.255][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.256][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:48:27.259][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.260][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:48:27.269][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.270][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:27.272][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.274][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.276][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.277][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:48:27.278][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:27.280][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.281][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:48:27.282][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:27.284][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.286][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.287][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.288][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:48:27.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.292][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:27.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.296][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.297][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.298][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:27.300][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:27.301][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.302][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:48:27.304][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:27.305][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.325][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[2023-11-02 08:48:27.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.409][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:48:27.411][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:48:27.413][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:48:27.415][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:48:27.416][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:48:27.418][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:48:27.420][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:48:27.422][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:48:27.424][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:48:27.426][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:48:27.428][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:48:27.430][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:48:27.432][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:48:27.433][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:48:27.435][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:48:27.437][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:48:27.439][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:48:27.441][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:48:27.443][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:48:27.445][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:48:27.447][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:48:27.449][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:48:27.451][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:48:27.453][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:48:27.455][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:48:27.457][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:48:27.459][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:48:27.461][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:48:27.463][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:48:27.464][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:48:27.466][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:48:27.468][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:48:27.470][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:48:27.472][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:48:27.474][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:48:27.476][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:48:27.478][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:48:27.480][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:48:27.482][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:48:27.484][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:48:27.486][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:48:27.488][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:48:27.490][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:48:27.492][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:48:27.502][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:48:27.504][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:48:27.506][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:48:27.508][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:48:27.510][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:48:27.511][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:48:27.513][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:48:27.515][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:48:27.517][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:48:27.519][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:48:27.521][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:48:27.523][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:48:27.525][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:48:27.527][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:48:27.529][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:48:27.530][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:48:27.532][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:48:27.534][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:48:27.536][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:48:27.538][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:48:27.540][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:48:27.542][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:48:27.544][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:48:27.546][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:48:27.548][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:48:27.549][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:48:27.551][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:48:27.553][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:48:27.555][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:48:27.557][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:48:27.559][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:48:27.561][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:48:27.563][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:48:27.565][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:48:27.567][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:48:27.568][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:48:27.570][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:48:27.572][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:48:27.574][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:48:27.576][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:48:27.578][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:48:27.580][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:48:27.581][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.583][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.631][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.DEBUG[2023-11-02 08:48:27.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:48:27.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.744][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-11-02 08:48:27.746][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-11-02 08:48:27.748][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.750][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.752][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:48:27.754][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.755][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.756][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.758][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-11-02 08:48:27.759][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-11-02 08:48:27.760][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:48:27.762][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.763][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-11-02 08:48:27.764][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-11-02 08:48:27.766][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-11-02 08:48:27.767][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:48:27.768][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:48:27.768][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:48:27.768][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:48:27.770][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-11-02 08:48:27.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.774][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:48:27.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:48:27.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:48:27.777][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:48:27.779][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:48:27.779][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-11-02 08:48:27.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:48:27.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:48:27.783][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:48:27.784][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-11-02 08:48:27.784][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-11-02 08:48:27.786][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:48:27.788][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:48:27.790][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-11-02 08:48:27.792][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:48:27.794][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:48:27.796][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:48:27.801][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-11-02 08:48:27.802][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-11-02 08:48:27.804][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-11-02 08:48:27.805][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-11-02 08:48:27.807][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:48:27.808][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-11-02 08:48:27.810][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-11-02 08:48:27.811][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-11-02 08:48:27.813][biodb::testThat]
biodb.INFO [2023-11-02 08:48:27.814][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-11-02 08:48:27.816][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:27.817][biodb::testThat]
biodb.DEBUG[2023-11-02 08:48:27.821][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-11-02 08:48:27.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:27.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-11-02 08:48:27.829][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:27.831][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-11-02 08:48:27.835][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-11-02 08:48:27.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:48:27.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-11-02 08:48:27.843][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:48:27.845][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-11-02 08:48:27.850][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-11-02 08:48:27.852][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:48:27.854][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-11-02 08:48:27.856][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:48:27.857][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:48:27.859][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:48:27.860][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-11-02 08:48:27.861][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:48:27.863][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:48:27.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:27.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:27.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:27.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:27.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:27.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:27.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:27.883][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-11-02 08:48:27.886][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:27.888][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:27.891][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-11-02 08:48:30.133][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-11-02 08:48:32.918][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:32.920][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-11-02 08:48:32.925][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-11-02 08:48:32.928][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-11-02 08:48:32.930][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:48:32.932][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:48:32.933][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-11-02 08:48:32.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:32.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:32.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:32.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:32.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:32.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:32.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:48:32.956][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:32.958][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:32.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.960][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:32.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:32.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.968][ef$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:48:32.969][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:48:32.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.972][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-11-02 08:48:32.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-11-02 08:48:32.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.980][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:32.981][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:32.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.984][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.987][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:32.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:32.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.993][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-11-02 08:48:32.995][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-11-02 08:48:32.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:32.997][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:32.999][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-11-02 08:48:33.001][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-11-02 08:48:33.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.004][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.006][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:33.019][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:33.020][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.021][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.024][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:33.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:33.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.029][ef$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:33.031][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:33.032][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.033][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.035][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-11-02 08:48:33.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:33.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.041][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:33.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:33.044][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.045][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:33.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:33.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.053][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:33.054][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:33.055][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.057][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.059][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:33.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:33.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.065][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:33.066][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:33.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.069][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-11-02 08:48:33.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-11-02 08:48:33.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.077][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:33.078][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:33.079][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.080][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.083][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-11-02 08:48:33.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-11-02 08:48:33.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:33.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:33.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:33.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:33.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:33.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:33.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:33.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:33.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:33.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:33.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:33.205][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-11-02 08:48:33.213][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:48:33.215][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-11-02 08:48:33.216][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-11-02 08:48:33.218][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:48:33.219][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:33.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:33.222][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:33.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:33.224][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:33.226][FUN] Functions in observer 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 387 ]
>
> proc.time()
user system elapsed
25.798 3.763 176.203
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.050 | 0.885 | 4.356 | |
| ChebiEntry | 0.291 | 0.063 | 2.532 | |